I have been worried about this situation for quite some time. I still pass 20/20 in both eyes but I am worried that, later in my life, my vision could decay below 20/20 in my amblyopic eye.
I haven't looked into it too far but I did find this "FAA Guide to AMEs" and it talks about issuing special issuances for amblyopia subjects on page 55.
http://www.faa.gov/about/office_org/...edia/guide.pdf
I am interested to hear about others in my / our situation.