The ECU has no means of knowing what the fuel pressure is at either side of the filter. It can only know if there is a problem with the injectors, coils, fuel pump or one of the sensors. I'm not aware of any injection system that measures fuel pressure.
With current emissions requirements there is no way you will ever see a bike with carbs again. Modern injection systems are generally very reliable and I for one prefer them to any carburettor. Once you understand how they work fault finding is not that difficult and whatever fuel fecked up the filter would have played havoc with a carburetor set up too, although refilling the tank would probably have fixed it.
2015 Scrambler Classic
2017 Supersport 937
1982 Pantah 500SL