I want to repeat that the files although altered are sonically intact and still perfectly usable.
Well, yeah. The audio data itself is never altered, just the metadata. And honestly most people except those in specific circumstances (like yourself) are never going to care about that part of it because the audio data is not altered.
If one downloads purchased music from services like qobuz or tidal may at some point be surprised that his files have been modified.
Again, wording here is important as you make it sound like it's altering the audio itself when audio data is not altered in any way, just the metadata.
Believe it or not, I'm actually in a similar situation as you. I use Beyond Compare to sync my music library between my main library, my backup library and my NAS library and because of how large it is (over 150,000+ FLAC and DSF files) I can't add any new metadata fields to it without creating a massive headache. Fortunately when I started building this library the majority of the audio analysis tags were added so it wasn't a problem. What eventually became a problem was the additional metadata audio analysis added like waveform, HDCD and more recently the audio CRC field which thankfully I can disable writing of those tags to files in MC (and then I simply clear them from the library).
To avoid this in your case;
1) Restore all affected files from your backup/secondary.
2) Turn off the audio analysis feature to avoid writing of metadata to those files. Also disable the
Analyze waveform and
Analyze for HDCD settings.
3) Turn off the
Write tool name in version setting.
4) In the Configure Auto-Import's dialog, disable the last option to
Write file tags when analyzing audio, getting cover art, and applying folder-based tagsThat should help avoid this if you really want to, though I have to say having the audio analysis data can be quite handy, especially for volume leveling and displaying dynamic range.