I have to agree that the reason Bean is crying is that he has been displaced. With cats, relocating a litter box can be a traumatic event! So think about long term where you want Sunny to sleep at night, and try moving her there now, so Bean can have HIS place back.

Now, what if the place you want Sunny to be in . . . Bean's old place. I'm not sure WHY Bean can't be down there when Sunny is down there in her crate.

Also, with Bean's crate, can you turn the gate facing the wall and put it close to the wall, so even if he tries and succeeds in undoing the latch . . . the gate can't open. May need something heavy behind the crate so he can't push away from the wall (I wouldn't put ANYTHING past a determined cat!)