Will Lyra remember Will after the Amber Spyglass?

Yes, of course. Near the end of the novel, Lyra and Will fall in love. Sadly, they have to separate, in order to save the worlds. However, they promise each other that every year they will go to the bench in the Oxford Botanic Garden in their separate worlds. She promises to do this "as long as I (Lyra) live".

Also, "she wondered whether there would ever come an hour in her life when she didn't think of him". The book shows that they will always love and remember each other.