As of Archive Shuttle 9.9 it is possible to disable the automatic cleanup process on the staging area.
It is recommended to keep the source system running until everything has been imported into target. Sometimes, customers will decommission source environments prior to all items being ingested into the target and this can lead to problems as it means that Archive Shuttle can not re-export data if the staging area cleanup has been executed.
If customer has a large staging area they can decide to not delete any data from the staging area.
A system configuration option has been implemented to control this functionality:

The system health page will show a warning when the staging area cleanup is disabled:

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