..... Will this mod affect our factory warranties?
Same as with any USA vehicle mod (the short form): If Ford can show that your otherwise 'warrantable' specific problem is
caused by your mod, then they don't have to fix
that specific problem under warranty (US Federal Magnuson-Moss Warranty Act; google is your friend).
In this case, the Ford diagnostics tools
will reveal the fact that the APIM has been reprogrammed to a non-OEM configuration and even the date and time that was done. That includes any 'roll-back' reprogramming you do to restore to the as-built condition in an attempt to 'hide' the mod -
every reprogramming upload has a date/time/program identifier 'stamp' attached to it. I do not know if Ford can detect the complete
history of uploads but they can certainly detect the latest.
An APIM warranty extension has been applied to many Escapes (clipped from the notifications section of my VIN-specific Ford Owner Webpage):
VIN: 1FMxxxxxxxxxxxxxx
FSA Title: SYNC WITH MYFORD/MYLINCOLN TOUCH - WARRANTY EXTENSION COVERING ACCESSORY PROTOCOL INTERFACE MODULE (APIM)
Field Service Action Number: 12M02
IMHO no one can know in advance if a future APIM problem would be denied coverage by this mod (the case-specific 'problem' vs 'cause' question) but if you're concerned about such, the conservative assumption would be "yes, the APIM warranty may be jeopardized" and you should not do the mod if that's important to you. The only way to get NAV with zero warranty risk is to buy a car with it from the factory.
And of course, but I suspect you already understand this, the 'bootleg' NAV itself has no warranty at all.