I went to hunt for some clefairy today, and when i found one i noticed i didn't have any ultraballs or pokeballs left. I haven't used any of them, and i am definitely certain i had 300+ ultraballs.
Before this happened, i had bought a ton of ultra balls for an event i was hosting in my guild, and as 999 is the maximum number of any item you can have, i mailed a couple hundred to my baby account, IGN - Mythicasiann. Once the event was over, i transferred everything over to my main account (Raika) and had about 350 ultraballs left. Now they're completely gone.