Essentially, when she appears in Roya the "mana body" reflects all of the experiences and alterations that happen to it and pushes it to the real world. Her skin tone and hair not changing is because it's more of a cosmetic and not an actual body altercation.
If she lost her arm in Roya, it's possible that she would lose her arm in the real world too. So with her hymen being broken if she had sex in Roya, it would reflect that as well in the real world. Because her body itself is altered, it's different from an injury that will just be closed by her mana, permanent altercations are also permanent in the real world.