Is the letter being submitted to AMCAS as one part of a letter packet, either a "Committee Letter" (which is in fact a packet) or a "Letter Packet"? If it is either a committee letter packet or a non-committee letter packet, then I am 100% sure it will be fine. Letter packets consist of two or more letters that are inextricably linked together, as if they were stapled together with non-removable staples, and it won't really matter what the computer thinks the names are.
Is the letter being submitted to AMCAS as a stand-alone letter? In that case, the AAMC might complain, because they really like names to match. That said, it will only cause a few days of delay, because that is how fast you can resubmit a letter to the AMCAS. So don't freak out, just wait and see whether the AAMC complains about the name.
Med schools likely will not notice or care. They will mostly just look at the letter itself, which contains the professor's name however she spelled it. Even if they do see the 2-letter version somewhere, so long as it contains at least one vowel it might be a nickname, who the hell knows.
