I just beat giovanni at the bottom of Pinkan City. After that i got teleported back to the sailor at Pinkan City. I walked to the Pinkan Ranger to get my Pokeballs back but he didnt gived them back. He wanted a Electabuzz and a Scyther. So i looked in my inventory and i automaticly got my Pokeballs/great Balls and Ultra balls back. But the 2 Masterballs from the Chrismas present were gone. The times before when i entered the zone i had to give him my Pokeballs but he allowed me to keep the masterballs. But now they are gone. I was kepping them so if a shiny ralts/abra or something appears i can catch it. I m really frustrated because i couldnt now that this would happen and it would take me a lot of time to farm pvp coins for new ones because I dont have that good Pokemon. Just want to inform about this Bug.

I just reloged and they are in my bag again. Maybe it was just a visual bug.

the same thing happened to me, but i lost all my pokeballs (including masterballs) forever :(