I've been trying to make exceptions to my blacklist by specifying ones that aren't in my favorites list.

For instance, one of my blacklist entries is nipple_piercing -fav:LendriMujina. But that doesn't seem to work, and faving a work doesn't change its blacklisted status. Do negative operators just not work for special tags?

You need to use fav:me instead of fav:LendriMujina - it's a constraint of how the blacklisting system works.

faucet said:
You need to use fav:me instead of fav:LendriMujina - it's a constraint of how the blacklisting system works.

That didn't work, either. -fav:me still even blacklists posts that I've favorited.

Re621 has an option to exclude items you've favorited from being blacklisted, in case you can't get it to work naturally

It worked for me, did you save the blacklist change for fav:me? If you did then it might be that you have your blacklist organized in a weird way or something.