In Mario + Rabbids kingdom battle, Beep-O has lost break abilities. I am going back to find chests I have missed but can’t get to some without break. Is this normal?
Yes, this is "normal" if you go through the washing machine to get to the level. Beep-O will lose the abilities that weren't available at the time you originally played through a stage when you use the time traveling washing machine.
Instead, what you need to do is go back to the level by walking around Peach's castle and use the canon for the level you want to get into.