I'm sure you're right and its a change in smell that has him confused. It sounds like you have a good plan. If you're comfortable maybe you could let him sniff and touch her. Maybe wait till after she's done molting and in a better mood. :)
Oh, I feel your frustration. I recently adopted a puppy from a local rescue group. There were a couple on their website that caught my eye so I filled out the adoption application. Turns out one of them was being fostered by my brother's neighbor (though I hadn't meet them) and he told them. I...