Letter of Recommendation Problem

I had my school career center submit three letters of recommendation to a school I applied through AMCAS. The school today sent me an e-mail saying that one of the letters was not written on a letterhead, and that they couldn't accept it. I got the letter from a professor last year, who is no longer employed by my university, and it seems that I can't reach him through his old e-mail either.

I fortunately have an extra letter that I can send, but AMCAS won't let me assign that to the schools that I already have applied.

If I have my letter author upload the letter to AMCAS, will the school have the ability to download the letter even though I couldn't assign the letter specifically to the school? or should I have him send the letter to the school directly through interfolio or something?