"You know I live here," Gene says, suspicion definitely coloring his tone. "But you also said we were going to your place." You can see the wheels turning in his head and desperately search for something to derail his thought process.
"Yeah, we both live here," you say.
Suspiciously, Gene says, "You're a girl, but you think that you live in the guy's dorm? There's only one possible explanation for that."
"Of course there is," you say. "They put me in the guy's dorm because I'm technically male. You know that already!"
That really was a good explanation. At least it makes sense and doesn't require that you remember being a guy before. It could even be true for real--maybe when Gene changed your crotch back to male, it really did change reality so that you live in the guy's dorm again. There was a big problem with that explanation, though--it was easy for Gene to check it. You have no way to know if it was true for real, since you have no idea what dorm someone with this body would really be assigned to. If it really was, you're fine. If it wasn't, all he has to do is follow you back to your room.
Still seeming a bit suspicious of you, Gene tries to kiss you. You get another idea and say "What are you doing? It's not as if I was your girlfriend or anything." With luck, he'd think that making your crotch male also changed reality so that you aren't his girlfriend, and he won't try to follow you back.
But again, the explanation *could* be true--but you have no idea whether it is, and it probably isn't too hard to check. You have to either get the flashlight back, or hope against hope that the plausible things you just said were true by chance.