I think I found it!
I pushed a potential fix in v0.98! I believe the bug was that it would only kill Hidden enemies, so if you had somehow revealed him - he would live!
Ok, I found a very weird glitch now. I went to kill the balrog alone and it just made three random enemies come back to life and killed them.
Beat me to it. The curse of development (fixing a bug creates a new bug) seems to have struck xD
Whoops! You're right, there's a bit of bad logic in my new code. I can fix that right up. Sorry for the trouble :)Fixed in v0.981!