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Recommendation: Don't make changes to 2 places at the same time.
If you made changes on the USB drives, when you re-connect them, click "Import Changes" (at least I think that's what it's called; I don't have a USB drive handy to test it out and make a screenshot for you!) That brings all the changes you made on the players back into the main collection.
If you're simply exporting the changes from the collection to the USB drive, to a standard sync / export.