This would be a question to ask your GM. However, I would say that either your darkvision bumps up to 90ft., or you get back the wizard bonus feat at 5th level. There's no way that you should lose out on a feat just because you already have darkvision.
As a GM I would say the opposite. you already have darkvision so the darkvision at 5th level does nothing unless it specifically says it bumps up existing darkvision.