You're absolutely right - amnesia in itself can lead to a lot of interesting questions about the nature of identity. That's what I love about Dollhouse, Eternal Sunshine, and a bunch of other stories that feature memory loss. (And now I'm curious about your original fic, NO PRESSURE.)

It's the "how can we make these characters have sex" aspect where I get confused. There are far FAR more convincing and less problematic ways to get characters in each others' underpants. So why use amnesia?