How about the DTC’s? Are those all gone and the CANBUS operates normally?
I don’t understand why you are saying using Europe settings and software. All Sync APP software is international, although the voice files, Gracenote files, Logo files are specific to each region. These are just broken down to region for simplicity. You should be using South America files in your APIM if you are in SA, not EU files.
A 2017 Escape would have come from the US, imported to your country? It would have come with Sync 3.0 from the factory, so this is probably what they are referring to. It would not have had Sync 3.2 from the factory. If the DTC’s are gone and everything works, I would disregard their suggestion about the APIM.
However, they are completely correct that the issue may be ‘rooted’ in the APIM. Depending on what you did there could have caused an issue. (We cannot discuss FMods JB due to legal reasons on this website.)