Issue
This article explains the details which can be obtained from the Core log file in Archive Shuttle 6.5 to assist with gathering information about migrations which are being filtered by a specific folder path.
Solution
The Core and EV Export modules need to have TRACE level logging enabled in order to view the detailed tracing around the filtering which is taking place.
If the logging is not enabled, it is likely that the following will be seen:

2014-06-24 07:41:00Z|1352| 12|TRACE|CreateArchiveShuttle.Core.WebServices.ArchiveShuttle|Initialized new ArchiveShuttle WebService Client on 172.16.5.202 
2014-06-24 07:41:00Z|1352| 12|TRACE|                                               Get|Fetching Module with ID: cadfda66-34ea-e311-b2a6-005056b86181 
2014-06-24 07:41:00Z|1352| 12|TRACE|                               SetCollectedEVItems|ModuleId: cadfda66-34ea-e311-b2a6-005056b86181 | EVCollector      | rowi01-ev-01    -> Getting SetCollectedEVItems [11 ms] 
2014-06-24 07:41:01Z|1352| 12|TRACE|                                         ProcessOK|Deserialization complete [62 ms] 
2014-06-24 07:41:01Z|1352| 12|TRACE|                                         ProcessOK|NULL checks complete [63 ms]2014-06-24 07:41:01Z|1352| 12|TRACE|                                         ProcessOK|Converted 30 items [825 ms] 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Elapsed: 0 ms 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Items in Total: 30 [2 ms] 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Not Null Items in Total: 30 [3 ms] 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Item groups: 1 [13 ms] 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Items in this group: 30 [14 ms] 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Chunks: [1] 
2014-06-24 07:41:01Z|1352| 12|DEBUG|                                       AddOrUpdate|Items in this Chunk: 30 [0 ms] 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                                       AddOrUpdate|Existing items from DB: 0 [157 ms] 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                                       AddOrUpdate|Existing items concat: 0 [157 ms] 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                                       AddOrUpdate|New items: 30 [226 ms] 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                                       AddOrUpdate|Starting BulkInsert of [30] Items and [30] EV Properties. [0 ms] 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                                     CheckItemData|Check of number of records in temporary Item and ItemEnterpriseVault tables was successful (30). 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                                       AddOrUpdate|Finished Bulk Insert [163 ms] 
2014-06-24 07:41:02Z|1352| 12|DEBUG|                               SetCollectedEVItems|Result: True 2014-06-24 07:41:03Z|5160| 13| INFO|                                 GetExportCommands|Currently exported (and not imported) for Link 0302fede-d64a-40f7-8de7-191029cd1fd1: 0 Bytes. Still below highWatermark of 20 GiB 
2014-06-24 07:41:03Z|5160| 13| INFO|                                 GetExportCommands|Currently exported (and not imported) for Link 42eddbb3-0faa-4cec-b68f-b085206ba609: 0 Bytes. Still below highWatermark of 20 GiB 
2014-06-24 07:41:03Z|5160| 13| INFO|                                 GetExportCommands|Currently exported (and not imported) for Link 756e8f99-00bd-4c9e-9ed3-fcfe785eae94: 1.69 GiB. Still below highWatermark of 20 GiB 
2014-06-24 07:41:04Z|5160| 13|TRACE|                             GetToExportForMapping|MappingId: [47] | ExportItems: [20] 
2014-06-24 07:41:04Z|5160| 13|TRACE|                             GetToExportForMapping|[1] chunks @ 1500 items (max) 
2014-06-24 07:41:04Z|5160| 13|TRACE|                       <GetToExportForMapping>b__7|Chunk: 20 
2014-06-24 07:41:04Z|5160| 13|TRACE|                                           Dispose|<< Retrieving Items for Container Mappings [435.3855 ms] 
2014-06-24 07:41:04Z|5160| 13|TRACE|                                 GetExportCommands|Got 1 commands with 20 items to export.
^^^ Here the correct number of items can be seen, but, there is no way to know how that number was derived.
If the logging is enabled, then more detail will be provided as can be seen here:
06/24/2014 10:10:06|6672| 38| INFO|                                               Get| -> Got 1 commands 
06/24/2014 10:10:06|6672| 38| INFO|                              ProcessManualCommand|Got Command CollectItemsForArchive with commandID 105 
06/24/2014 10:10:06|6672| 38|DEBUG|                                          GetEVDAL|EV Version 10 SP4 Detected. Schema Version is 10.125.5.137 
06/24/2014 10:10:06|6672| 38|DEBUG|                                  GetWigForArchive|Returned existing WorkItemGroup for ArchiveID 1484D0B45BD1D5C4A90D3983DE6F6B8681110000rowi01-ev-01.rowiev.local 
06/24/2014 10:10:06|6672| 38|DEBUG|                                          GetEVDAL|EV Version 10 SP4 Detected. Schema Version is 10.125.5.137 
06/24/2014 10:10:06|6672| 38|TRACE|                                           Dispose|<< Collecting Items for Single User [10.4984 ms] 
06/24/2014 10:10:06|6672| 38| INFO|                      CollectItemsForSingleArchive|Collecting Items for Archive [foder2] 
06/24/2014 10:10:06|6672| 38|DEBUG|                            <CreateThreadPool>b__7|Number of commands in thread queue 0. 
06/24/2014 10:10:06|6672| 38|TRACE|                      CollectItemsForSingleArchive|8786d3c7-3711-43f1-8503-5703a2144834 added successfully to ResultDict 
06/24/2014 10:10:06|6672| 38| INFO|                               GatherArchivedItems|*** Starting Collecting Items for foder2 from: 01/01/1900 00:00:00 
06/24/2014 10:10:06|6672| 38|TRACE|                               GatherArchivedItems|Collecting [30] items for Archive [foder2] 
06/24/2014 10:10:07|6672| 24| INFO|                               GatherArchivedItems|Finished Item Collection for foder2 
06/24/2014 10:10:07|6672| 10| INFO|                               GatherArchivedItems|Parsed 30 Items 
06/24/2014 10:10:09|6672| 12| INFO|                        TransferItemMetadataToCore|Starting transmission of 1 containers containing 30 items to core 
06/24/2014 10:10:09|6672| 38|TRACE|                        TransferItemMetadataToCore|Checking Container: 8786d3c7-3711-43f1-8503-5703a2144834 
06/24/2014 10:10:09|6672| 38|TRACE|                        TransferItemMetadataToCore|Adding container 8786d3c7-3711-43f1-8503-5703a2144834 to transmission list. 
06/24/2014 10:10:09|6672| 38|TRACE|                                             .ctor|>> --> WT: Sending 30 Collected Items Metadata to Core for 8786d3c7-3711-43f1-8503-5703a2144834 
06/24/2014 10:10:09|6672| 38|TRACE|                                             .ctor|>> --> WT: Sending 30 Collected Items (chunk) Metadata to Core for 8786d3c7-3711-43f1-8503-5703a2144834 
06/24/2014 10:10:09|6672| 10|TRACE|                                             .ctor|>> SetCollectedEVItems 
06/24/2014 10:10:09|6672| 10|TRACE|                                             .ctor|>> CallWebService 
06/24/2014 10:10:09|6672| 10|TRACE|                                    CallWebService|Communication attempt number: 1 
06/24/2014 10:10:09|6672| 40|TRACE|                                           Dispose|<< CallWebService [169.1738 ms] 
06/24/2014 10:10:09|6672| 10| INFO|                                          SenderWT|0/30 items still in this transmit queue. Chunk: [173 ms] Total: [173 ms] 
06/24/2014 10:10:09|6672| 10| INFO|                                          SenderWT|Core Transmission finished. Success: 30 items | Failed: 0 items. [173 ms] 
06/24/2014 10:10:09|6672|  9|TRACE|                                    CallWebService|Communication attempt number: 1 
06/24/2014 10:10:09|6672| 40|TRACE|                                           Dispose|<< CallWebService [172.5856 ms] 
06/24/2014 10:10:09|6672| 38|TRACE|                                           Dispose|<< SetCommandResult [173.1183 ms] 
06/24/2014 10:10:09|6672| 38|TRACE|                                           Dispose|<< --> WT: Sending 30 Collected Items Metadata to Core for 8786d3c7-3711-43f1-8503-5703a2144834 [347.303 ms]
From Core:
2014-06-24 09:10:11Z|5160| 26|DEBUG|                                   GetCommandsImpl|GetCommands | moduleId: c7dfda66-34ea-e311-b2a6-005056b86181 | commandCount: 10 | Host: rowi01-ev-01 
2014-06-24 09:10:11Z|5160| 26|DEBUG|                                   GetCommandsImpl|ModuleId: c7dfda66-34ea-e311-b2a6-005056b86181 | EVExport         | rowi01-ev-01    -> Retrieving Next 10 Commands 
2014-06-24 09:10:11Z|5160| 26|DEBUG|                                CheckDataLicensing|Link licensing still valid 
2014-06-24 09:10:11Z|5160| 26|TRACE|                          GetAssemblyLoadDirectory|AssemblyLoadDirectory: C:\Program Files\QUADROtech\Archive Shuttle\Webservice\bin 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                             Check|Checking License... 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                               Get|Fetching Module with ID: c7dfda66-34ea-e311-b2a6-005056b86181 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                  NeedsItemRouting|Get ContainerOperations for [17] mappings. 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                  NeedsItemRouting|Get Containers where we need Initial Routing 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                  NeedsItemRouting|Got [0] Containers for Initial Routing 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                  NeedsItemRouting|Retrieving Containers which need Item Routing. 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                  NeedsItemRouting|Routings needed: 1 | not needed: 16 | checked: 17 | mappingIds: 17 
2014-06-24 09:10:11Z|5160| 26|TRACE|                           GetSqlCommandForFilters|Filtering by Path. 
2014-06-24 09:10:11Z|5160| 26|TRACE|                           GetSqlCommandForFilters|Sql Command: Path NOT LIKE @Pathvalue1
^^^ Here the filter operator can be seen, in this case it is NOT LIKE. This means all folders except the one specified below will be migrated.
2014-06-24 09:10:11Z|5160| 26|TRACE|                           GetSqlCommandForFilters|Sql Parameters: 
2014-06-24 09:10:11Z|5160| 26|TRACE|                           GetSqlCommandForFilters|Name: @Pathvalue1 | Value: Fred123 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|SQL Command: IF OBJECT_ID('tempdb..#TempTable') IS NOT NULL DROP TABLE #TempTable;SELECT TOP 5000 Item.ItemId, @mappingId as ContainerMappingId INTO #TempTable FROM Item LEFT JOIN ItemRouting ON Item.ItemId = ItemRouting.ItemId AND ContainerMappingId = @mappingId INNER JOIN StoragePath ON Item.StoragePathId = StoragePath.StoragePathId WHERE ContainerId = @containerId AND ItemRouting.ItemId IS NULL AND DeletedDateUtc IS NULL AND Path NOT LIKE @Pathvalue1; INSERT INTO ItemRouting (ItemRouting.ItemId, ItemRouting.ContainerMappingId) SELECT * FROM #TempTable  
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Sql Parameters: 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Name: @mappingId | Value: 48 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Name: @containerId | Value: 8786d3c7-3711-43f1-8503-5703a2144834 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Name: @Pathvalue1 | Value: Fred123
^^^ Here the filter value (eg folder name) can be seen, along with the container mapping which is being routed.
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|SQL Command: IF OBJECT_ID('tempdb..#TempTable') IS NOT NULL DROP TABLE #TempTable;SELECT TOP 5000 Item.ItemId, @mappingId as ContainerMappingId INTO #TempTable FROM Item LEFT JOIN ItemRouting ON Item.ItemId = ItemRouting.ItemId AND ContainerMappingId = @mappingId INNER JOIN StoragePath ON Item.StoragePathId = StoragePath.StoragePathId WHERE ContainerId = @containerId AND ItemRouting.ItemId IS NULL AND DeletedDateUtc IS NULL AND Path NOT LIKE @Pathvalue1; INSERT INTO ItemRouting (ItemRouting.ItemId, ItemRouting.ContainerMappingId) SELECT * FROM #TempTable  
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Sql Parameters: 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Name: @mappingId | Value: 48 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Name: @containerId | Value: 8786d3c7-3711-43f1-8503-5703a2144834 
2014-06-24 09:10:11Z|5160| 26|TRACE|                                       AddRoutings|Name: @Pathvalue1 | Value: Fred123
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