My guess would be no, but that's just a guess. auto_incrementing fields can't have duplicates as you know, but when the engine is told to change a field to auto_increment, does it check to see if dups exist? If it does and there are, I'm sure it would choke. And it should (!) or else your talking about a potential corruption of data.
Shouldn't be any problem at all if the column is Unique (Which it is if it is a primary key and not composed) and of some Integer type... Take a backup of your data before trying anyway to be safe..