Up until FTM2010, the uploading and downloading from your AMT (Ancestry Member Tree) was NOT Family Tree Maker friendly, or with the use of a GEDCOM for the download piece. GEDCOM does not have images. So you are right there.
With FTM2010, uploading and downloading was FTM friendly, meaning images and all.
What should have happened, with FTM2012, depending on where your Master File was (the most current file with images) is that file should have been Downloaded and Linked from AMT to FTM2012 or from your FTM2009 file into FTM2012 version, then uploaded and synced to a new AMT.
YOU have to Back Up the file, as you go, using the File, Back Up command. Not sure what the "we thought we were backing up everything as we went" happened, unless you backed it up.
Can you Identify the Most accurate, most complete file, with your sources and media files?
I am not sure what you are trying to do all of this merging. Merging can be a night mare. What are you trying to merge?
Do you have a Good file on Ancestry? That has everything you want?
Do you have ONE file on your PC that has everything you want?
If not everything, as close to everything as you can, without Merging?