I’m not an expert in this but in the link below (and the link from above) a lot of people have investigated the APIM, As Built Data, and the MicroSoft software for Sync 2 with respect to navigation. The bolded / underlined / italic text above is telling. If the ABD for navigation gets changed / corrupted (including checksum) in the APIM, recovering from this appears to be above the “dealer pay grade” as vehicle may indicate car never had navigation. Dealer can access Ford ETIS which will show how the car was originally equipped (with / without navigation). I don’t believe the Ford ETIS can be changed. So, dealer must have screwed up since you had navigation and now you don’t. From what I have read in other forums, it appears sometimes the APIM needs to be replaced to recover navigation.
You should also go back to dealer and ask for a printout from ETIS showing the ABD. This is what the salesman / tech should have used to determine how car was originally equipped.
Again, I would open a case with Ford directly to resolve issue.
https://forum.xda-developers.com/windows-mobile/general/myford-touch-hack-enable-features-t3321397