yorkiepudding,
Sorry, other side of the pond, But my ancestors left a fine tasting beer behind, or so I am told.
If you Unlink your AMT from your FTM2012 file, you can always Upload and Link to a NEW AMT on Ancestry.
A GEDCOM does not come into play here.
You CAN download a GEDCOM from your online tree AND you can generate a GEDCOM file from FTM2012, but that isn't what you are trying to do here.
Russ