Just earlier today I tried battling the mysterious trainer, figured I'd have the wrong pokemon in first slot, went to team page and replaced it (jirachi) with my golurk with toxic. I went back to the myst. trainer and for some reason i had a jirachi in the slot the golurk was in previously (4th), but also in the first slot - a perfect clone of my rachi, making my golurk gone :|

Is this already known or is there any way known of recovering the pokemon lost in this way?

If not, fixing is needed.


Edit:
I also realized that almost all the time i Log out and log in again, the last pokemon in my team is stored in the box for some reason, randomly. Maybe those two are connected somehow?

Send your slots 2-6 to your box and then remake them and it'll be fixed

Spelling mistake:
a perfect clone of my "rachi", making my golurk gone :|