I got a similar “issue” with metadata not being written, but it always looked like coincidence rather than a rule. sometimes, md would be written, sometimes not, and the files with the signaling tags were here and there, even when all images were in the same folder.
Timing might be a cause for this erratic pattern and maybe the solution is to simply write md again, as I do manually. NLP can possibly do the same, e.g. trigger a rewrite when closing.
Ok, thanks for double checking this and all for all the details you provided earlier.
I’m not able to replicate this on my Apple Silicon MacBook, so it might be something particular to your setup.
A few other things to try:
Update Lightroom Classic to the latest version
Try resetting Lightroom Preferences (which will require reinstalling NLP). This can sometimes clear out issues.
If you have any raw files that are not through Vuescan, see if you encounter the same issue with those (it could be something particular to the metadata there).