After moving my core to a new server and restoring my last backup, everything works fine (music folder has not moved) but when I move my album folders to a new location on the same usb hdd, I loose metadata like number of plays and favourite albums.
If you have a backup from before you added the dupes, I would recommend restoring that and then following these instructions.
If Roon was watching your files in two places at the same time, that can potentially cause some problems, as Roon will be tracking two copies going forward.