James,
You are correct...no surprise.
When the Capture action to the archive stored on the SMB mount point fails, the archive is left damaged...and must be repaired first. This was automatically happening before...since I always ran a Verify action after the Capture failed...and the Verify fixed the archive's data component.
My error, in this case, was attempting to reindex of the archive before manually repairing it...(or running a Verify)...and it, therefore, failed, as you stated because the data was damaged by the Capture.
I repeated my steps...after first copying a clean archive to the SMB share...
1) Running a Capture...which failed.
2) Repairing the now damaged archive on the SMB share
3) Deleting all the .index files in the package
4) Reindexing the archive...which did work fine.
5) Trying another Capture...which failed.
So...at this point, I believe it is still only the Capture that has the issue to the SMB share.