Ok, first off, I hope you didn't save in the rift. I found the best way to beat difficult rift bosses is to use a chessy tactic, like a destiny bond user or even perish song. Do you have Pokemon that can use moves like that? What is your team currently?
Oh, ok. That sounds like a glitch. You should post your file on the save file trouble shooting forum. someone there should be able to fix it up good as new.
