could you provide a link to this tuning box? they shouldnt do anything apart from overridng the fuel rail, pushing more fuel into the system to provide a hacked way of more power.
they should be writing anything to the ECU unless it was a proper remap
make sure you fit a GENUINE FORD fuel filter, ive tried two aftermarket ones before and they both gave me issues. you will need to go to a ford dealer to get one, or order from www.fordpartsuk.com