The users with Linked Mailboxes are not shown in the Archive Shuttle UI.
The log snippet from ArchiveShuttle.WebServiceLog.Hostname.ADCollector.Core.txt or ArchiveShuttle.WebServiceLog.txt log file is showing us that we are not adding the linked accounts in the database as we are missing the master accounts. Without the master account, we are not able to add the linked one.
2015-03-30 11:16:44Z|2156| 42|TRACE| AddUser|User has linked Mailbox (msExchMasterAccountSid is set to 'S-1-2-34-567890123-456789012-3456789012-345678', user display name 'TestUser'), but master account is not yet in our Database. Skipping.
This relates to how Archive Shuttle is connecting Master Accounts from the resource domains with Linked Accounts in the target domain.
AD collector config “IgnoremsExchangeMasterAccountSid” should be set to True (default value False) on Resource domain with Exch on-prem mailboxes and disabled users to collect those mailboxes.