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Thank you for the reply.
Auto merging may be the culprit for the imported files not equalling the files in the original source folder. How does that explain the empty folders and left over files not added? I know its something I'm overlooking but I've tried to troubleshoot where I could and came up with nothing.
There are no sub folder in the source folder.
You've given me some things to look into, so I'll check back with my findings.
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