Bah, it's a shame if the glitch happens during the replay and not after it is saved.

It probably would be possible to still make it work if after you were done with it and before closing the client window you ran the replay through this script: http://forum.toribash.com/showthread.php?t=439010 , but I'm still not sure. Plus that would require you to play really safe and use the script every time you finished a replay, just in case it was glitched.

My best advice is probably to make multiple save files and periodically check them while you're making the replay.
That and trying to talk to hampa about it. It's a shame that we still don't have a convenient way to report bugs, but you can always try and post it on the Beta Releases forum (maybe??) or talking directly on irc to him about it.

We can also try and figure out a way to recreate the glitch, but I'm not so sure how to do that. Got to discuss it with NutHug to see if he has any crazy ideas.