I'm not sure what program you're all using to tag FLACs, but here's what I do (and why)...
I create a batch file (.bat) that adds all the tags using the DOS command prompt using metaflac.exe
I then save all the batch files that I do, and it's easy to store all of these, as it's essentially just a text file.
so, at any point in time, say, if my harddrive crashes and I go back to my archived DVD to restore the data to a new HD. but the archived DVD is the untagged version. it is then trivial to add all the tags back. just double click each .bat file, and with 2 or 3 seconds, all the FLAC files are re-tagged. or, if you want to seed a show, but for some reason, you want to seed the "untagged" version because that is already what's "out there", you can easily remove all the tags with the "metaflac --remove-all-tags filename1.flac filename2.flac" line. then, when you're done seeding, just re-tag with the saved batch file. or, even better, just make a copy of the tagged files, strip the tags from the copy, seed, and then delete the untagged when you're done seeding.
if you want to check out what my batch files look like, I've attached one of them.