Hmm... This has always been a bit of a bone of contention between the two sides. I've been taping since my WM-D3 days (although I've been on a bit of a sabbatical the past four) so I feel I have some insight on this.
I mean, I remember the days where many of us were backing old analog tapes > DAT at either 48k, 44.1k, or even 32k and there was a huge divide on what the "correct" sample rate was (I used 32k for a lot of stuff just because the audience analog tapes I had didn't really have the dynamic range to warrant wasting tapes).
Regardless of my sidetracking, I think a valid point was made. As long as your md5 file has a matching crc between your WAV and FLAC files, you're pretty much assured that "nothing" has happened to your original file.
That's not to say that you shouldn't keep a copy of the original non-FLAC'ed WAV somewhere else as it's a "true master". Probably the idea of archiving your FLACs to an external hard-drive makes more sense than burning those to a DVD as well (if you're burning the originals).
DVD's can be finicky from one drive to the next (my wife's Toshiba Laptop burns discs that my HP Laptop tends to get nervous over - and vice versa - and both drives are made by Panasonic). The best way to do this is to back the files up on a physical drive (for instance, I'm fortunate that I can pick up a 250GB WD 5400 RPM "Passport" external drive for $120 at Costco in Canada). That's A LOT of FLAC files.
On another note, I recorded a lot of shows in between 2001 and 2004 on MiniDisc (with lossy compression). The recordings were then transferred via Analog to my PC (using a relatively hi-end audio card). All of my shows were burned to CD using CDRWin and were track-split to WAVs to create FLACs which were archived on Mitsumi DVD-R media. I have no real problems, personally, with using FLAC. I like the fact that it shrinks file sizes without affecting playback. The only other option you have is to look at Apple Lossless (
http://en.wikipedia.org/wiki/Apple_Lossless) which a friend of mine is using to archive his entire CD collection to a 1TB hard drive. You can play these files back on your iPod without issue as well which makes it convenient.
Hope I've added some food for thought.