Just had this happen to me today. went here to post about it but it seems that won't be necessary xD (although it's clear this hasn't been addressed properly.)
just happened twice during Sanctuary Onslaught as I was leveling a brand-new Yareli.
- Was riding Merulina
- pressed 5 for Transferrence
- instantly, Yareli disappears, and there is no way to return to her
- also, Operator is now invincible (kinda hilarious) and is ignored by enemies
- all Affinity progress I made with Yareli and my equipped weapons was lost. (In fact, the mission results screen was devoid of any information)