You will have to draw out your current Sage X3 folders setup first. What is the copy folder set for each folders.

If all folders root and copy folder is X3, then all are distinct unless you modify X3 folder.

If there is Copy folder set to a folder, check the Copy data section for things copied over from Copy folder to this folder.

I dislike preparing a dedicated copy folder since it imply the need to also additionally backup this copy folder as well and introduce coupling requirement (no copy folder, assume fail disaster recovery) but from your requirement, you may want to consider it depending on how much folders we are looking at. Do note that I do not have experience in using it in live environment despite being part of Technical Consultants certification requirement.

For me, I would just manually do it and charge manual technical effort per folder.