Previously the YADB track info database has worked pretty well with the individual tracks that I have personally submitted, but it seems to be broken at the moment. I have reported about this in the MC11.1.200 thread and in the MC12 forum.
However, this database contains only basic tags, not everything you have in the library. I use the following system for preserving all library info.
First I make a playlist of the old files and change the file names from e.g.
"01 - Song A.mp3", "02 - Song B.mp3, "03 - Song C.mp3" to "01.ape", "02.ape", "03.ape", etc
with the Rename Files From Properties and Find And Replace tools. I.e. I change the old names to plain track numbers and force the filename extension to be ".ape" (I use APE, but this should work as well with FLAC).
When I re-rip files I use a different library, a separate ripping base folder, the Artist\Album folder structure and plain track numbers as the naming rule. I don't do a YADB lookup. I fill manually the Artist and Album fields quickly with something short that I can recognize later.
After I have ripped the files I replace the now wrongly named old mp3 files in the original album folders with the new APE files. I move the files outside MC.
"Update Tags From Library", "Update Library From Tags" and "Rename Files From Properties" are the last steps (the order is important).
If you want to preserve the old files you can backup them and the library before doing this procedure (which you should do anyway). After re-ripping move the FLAC files to a different base folder (do this inside MC) and restore the backups (the media files as they were and the library backup to a new empty library) so you can use both libraries.