
Well, if their symbiotic control is re-functioning now that she's up then they might be partially aware of what's going on with each other still. And since by then he was already learning to be a warrior they may have decided to leave it rather than unnecessarily interrupting his training. And deal with the issue when they decide to re-meet.

I disagree with you on one point, the female side could've still explained that it was her twin trying to help her. It's really stupid to just agree and make the male side a criminal. Because that makes meeting up much harder. As soon as he enters the city or meets anyone that saw him "attack" the female side, he'll be regarded as a pervert and criminal and end up being attacked. Then even if they do meet up, they'll have to explain everything as well as explain the reason the female side told them she was attacked when now they're saying that they are siblings. It's better to deal with things straightforwardly then leave it be, creating misunderstandings and trouble.

Let's also not forget about the absurdly stupid logic of the guy that attacked. "A young man is holding an unconscious young woman! He must be a pervert and a criminal!" I mean really? That's the first thought you have when you see a situation like that, and you decide to immediately attack and try to kill the guy?
This person (this persons?) lacks any logic... As soon as "she" woke up "she" should have just quickly explained that the "guy" was "her" twin brother or something.
If this was me, I would have gotten pretty damn angry at the people "rescuing" the female me, yelling at them that they had attacked my "twin brother", whom was just trying to help, and demanding that they find him as soon as possible.