Pokemon glitching out in pc

Pretty simple. I caught a wild eevee (earlier today), it had bold nature for those of you who know what I'm talking about. I had it in my pc, nothing was wrong. Then I was in a little tournament thingy, and after getting second place the person traded me an eevee with a leaf stone. I got it and put it by my other eevee's. As soon as I put it in there, it deleted the eevee I caught earlier. Note the eevee I got ended up being the same eevee I caught earlier, so I'm assuming that has something to do with the pokemon going away.

I wasn't going to post this cause I didn't have proof of having both eevee's at the same time or anything like that, but Barry told me this was a known issue and I should post it. For any staff wondering, the eevee in my pc (5th page) that has bold nature is the eevee I'm referring to. If there's something you see that shows my pokemon glitching out or something, please let me know. I know for sure though when I placed it in my pc I saw the other eevee go away randomly.

I have checked every page and made sure it is gone. No items were on the lost eevee, and it was literally the same as the one in my pc. I believe the eevee is lvl 34, and it has bold nature. You can see in my pc it says obtained by trade, as the one i caught isn't there. If you need to check my trade logs (if you can), then go for it. When I traded for the eevee, I made sure I was trading an abra (not my eevee somehow).

If there's anything else I can do to help fix this issue, please let me know. It's not even a good eevee, but since it did glitch out and went away I hope there's a chance I can get it back.

(This was on server 19 btw)

Thanks,
IGN: Therobodavo