Glad to help.
It's not that MC "didn't mind" differences in filenames before: it's either that there were no differences before, or you didn't notice that some files weren't working.
So if you are seeing discrepancies in the file names that were not there before, then either the file names on the disk or the file names in the library were changed between before and now.
In order for a library file to be playable by MC, the filename (and path) recorded in the library must EXACTLY match the actual filename and path on the disk. Period. If the filenames are different, even slightly, they are just not the same file. If the filename listed in the library is wrong by even the tiniest bit, it is wrong, and the file does not exist (by that name).
This full file specification (path+filename) is called the "link" in MC. If the link is incorrect (broken) then MC cannot find the file when you try and play it. It's that simple. There is no such thing as a small difference: any difference whatsoever means the link is broken, and the result is total failure.
If you had autoimport running with the "fix broken links" setting turned on, MC might have been finding and trying to fix the broken links for you behind the scenes, but they were still broken until MC fixed them. If this was happening, it's because the files were being changed or moved on your filesystem outside of MC: that's bad.
You do not need to actually try to play the file to see if the link is broken. MC will show you with the icon (it will be a little red do-not-enter sign with a white line across it). And MC provides you additional tools to identify library entries with broken links... Take a look at this article:
https://wiki.jriver.com/index.php/Broken_LinksThis step should not have been necessary based on your original description, that you had everything backed up "Same names, same folders, same locations". It would appear that was perhaps not the case, as now you're talking about filename differences, and therefore you have broken links. You can use the info above to quickly find all the problems. Fixing the discrepancies will be a manual process.
Going forward, I recommend you write your tags to the music files. That way, your metadata is saved both in the files and in the library, so you won't have to ever re-tag. If the library is lost, a new empty library can read all the metadata from the files. If the files are lost, and replaced with untagged backups (why? backup the tagged versions!) then the metadata is in the library and can be rewritten to the tags in the files (what you should be doing now).
Good luck...