Organization, subs, moving files, library

I have a strange setup. My sources were/are a mess.. older recordings from Plex, new content recorded via PlayON. Some folders looked great.. movie named subfolders with content inside. PlayON recordings had to go through a renaming script (thanks AI for scripting). Some had no subtitles. I recently talked AI thru making me PY scripts to use WHISPER to add subtitles.

While doing this I found a lot of MP4s and MPG movies stored flat in one the parent MOVIES folder. AI made a script to stick them all in their own subfolders.

My Channels library, even though I asked for a rescan and to prune removed media..now sees both copies of the movie but playing the one tied to the old flat location fails.

Is my only remaining option to remove all personal media folders and then to re-add them to channels? Will removing the old personal media folders remove the stored channels files?

This is a Win10 PC doing all this with a 3060 (or is it a 3070?) vid card.