It makes no sense Mikasa had no idea what Eren wanted to do before she killed him, so it was then when she remembered the time in Paths.

But she didn't remember that, she experienced that right then and there. She was in paths with Eren for potentially years, while sitting on Falco's back.

Something that never should have happened as Eren couldn't have erased her memories.

He didn't erase her memories.

It went like this: Mikasa on Falco -> headache -> Mikasa in paths with Eren -> Mikasa leaves paths, kills Eren.

Eren neither erased nor altered her existing memories. She just "added" a new memory, the memory of living with Eren. But that occurred naturally.