I would...
Check each affected library field and make sure the setting "save in file tags (when possible)" is checked. To do this, go to "Tools > Options > Library and folders > Manage library fields"
Once happy with that, select all files, then run "Library Tools > Update Tags From Library" on the lot. Depending on how many files we are talking about, this could take some time.
Now, your file tags and your library will be in sync, and, so long as you have not turned off tag writing in MC, will stay in sync and you won't bump into this issue again.
Maybe test a small subset first if you're nervous about this.
As you correctly worked out, the automatic library backups are your friend, and they work very well. You can make manual backups too, if you like, immediately before testing, and restore from those.
Just shout if you have any more questions...
-marko.