I tried your alternate Build Missing Thumbnails directions and that process is running now ..
Great! Probably best to wait for that to finish before doing the stuff below.
Re: duplicate files... Under standard view I tried several of the albums but no red icon appears next to select files ( although I am sure I saw that happen earlier in different list view!). HOWEVER ... In several albums in ALL CASES one duplicate played ... the other did not.
In that case, try this. First, make a new backup of the library in case this doesn't go the way you want.
Then check that Auto Import now has all the correct settings under the "Folders" heading. i.e. That is is only pointing to the Y:\ drive which is your NAS for music files, and check the detailed settings under each watched folder to make sure you are happy with them. i.e. You don't want to be importing Video files that MC finds under a Music directory, and you probably don't want to be importing music files found under a Movies directory. All this is probably correct since you loaded your Library backup, and it should have been correct in there.
Then check the setting at the bottom of the Auto Import configuration called "Fix broken links".
If it is set to "No", then change it to "Yes (protect files on missing drives)". Then run Auto Import and see if some or all of the duplicates go away.
If it is set to "Yes (protect files on missing drives)" or the duplicates didn't go away when you ran the Auto Import above, set it to "Yes" and run Auto Import again.
If the above totall y messes up your library, restore the backup you just made.
BUT, wouldn't it be possible to just keep the current Library and Settings , delete all the music files... then reload the music files from the NAS? You will recall that I still have to do an upgrade to jrmc 23.
If the above doesn't work you could "Clear" the library, for which there is a button when you select the Library under Playing Now. There are a few things to consider though.
All the thumbnails you are currently building would have to be down again. MC won't reuse those.
Clearing a library also deletes all Playlists, so if you have any of those from the earlier library you want to keep.
If there are tags for any files in the library that could not be stored inside the files, you could lose those. They should be preserved if the MC Sidecar files are left in place, if there are any. That depends on the format of the files. For WAV files it could be an issue. For FLAC, MP3, APE etc. files it shouldn't be a problem.
Probably less important, but I'm not a fan of the brute force approach because of unknown side effects. But you would have the backup you just created above, so you could restore it to undo the Clearing, if required.
You could also just select all audio files in the Library and delete them from the Library, being careful not to also delete them from your NAS. Note that if you do this you will need to make sure MC will re-import them, either by turning off the Auto Import setting called "Ignore files previously removed from the library", or by deleting the record of the deletion from the special database in MC called the "Removed" database. I can explain how to do that later if you want to go down this path. Thumbnails would stil be built in this case, and you may stil lose some tags, but probably not. Playlists would remain safe though.
Bottom line, if the Auto Import settings don't fix all or most of the problem, then Clearing the library, or deleting all audio files from it and reimporting is an option.