check out the vaulted copies of the files and then overwrite the local copy with the one from your folder (copy/paste, move, or save-as). then check them in.
We have a utility that can help you out, we use it for a lot of EPDM data migrations. It can resolve duplicates, heal drawing title blocks, find missing references, automatically import your data into EPDM, rename your files (remove revision is most common), restructure your folders, populate your data cards from multiple sources, and properly set your revisions and lifecycle states.
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Hope this helps,