I found a duplication glitch by accident by catching some Loudreds before a server reset. I caught the loudreds and they went in my PC. I went to go get some xp and it said that my egg was getting xp for some odd reason, as if it was the loudred, even saying that the Egg was learning the move when it was actually a loudred. After that, the server reset. When the server came back up, the 3 eggs in my party were replaced by duplicated loudreds. I do not know very much about coding and I am hoping this helps.
Hello MVP, I've done some research on this issue. It's a known issue with Pixelmon, and the Pixelmon Devs are aware of it. That being said, we, unfortunately, can not replace any Pokemon lost to bugs and glitches in the mod as per our No Refund Policy. If this were single player, you would most likely shrug it off and continue on your journey to be a Pokemon Master. Not to mention our 1.10 servers are still highly experimental and bugs are still prevalent. That being said, to help avoid this issue in the future, we suggest when you see the 5 Minutes till Restart Warning that you wrap up what you're doing and give the server enough time to properly save your progress.