When your pokemon evolve after you exit the gui containing boss drops, you're stuck in a position in which you can move your mouse around but not wasd. Your pokemon does not evolve and when you/suicide, your pokes are stuck in their non evolved stage. Hopefully this can be fixed asap Steps to reproduce: 1: Enter a fight with a boss pokemon with a pokemon about to evolve 2: Defeat the boss 3: Obtain loot 4: Exit loot screen 5: If your pokemon obtained enough xp from that battle, it shall leave you bugged
It was a know issue, that they say was fixed. Not sure if they are talking in Beta 7 but. Pixelmon Mod Bugs - Pixelmon Mod - Bug tracker - Ticket #10132 - Boss Pokemon Evolution Error says already fixed, so maybe you should make a new ticket there.
Whenever It happens to me I just relog (it lets me use the esc key to get out) and when I get back in I just lvl up my Pokemon again with something other than a boss and it works fine.