I've been using carriers a lot. I know beams are over-powered right now, but I *love* the swarms of little fighter pummeling the crud outta the baddies - especially the Yor since they're always declaring war on me even if they've not met me.
Anywho, I had several fleets on course to attack some Yor at the same time I was about to finish researching beam weapons. I wasn't paying much attention & hit auto-resolve on all the combats only to be horrified when I discovered every single one of my fleets was wiped out! Then the game crashed.
Reloaded the auto-save. I couldn't target any Yor ships; targeting allies still brought up the "you sure?" The next turns I was able to wipe out everything that had wiped me out previously.
It then occurred to me that maybe all my fighters had "lost" their beam weapons due to the upgrade (since the graphix went from red beams to yellow beams) & so nobody did any damage (my carriers are currently unarmed.)
I made a copy of that auto-save but the inability to target any thing with combat ships means I'm not able to verify what happened. If you want the save file, just let me know & I can bundle it along.