It would be interesting to know which codes came together with the MIL/CEL.
Correctly mounted filter: The return line from the injection pump attaches to the "thermo tee" on the filter, supplying already filtered, heated fuel back into the filter and taking any excess back to the tank. The fuel that re-enters the filter has to go through the filter element again (I do not have a cut-away pic of a filter but the location of the connectors on top of the filter suggests this; unfiltered fuel is near the filter wall, filtered fuel comes out center).
Mounted the other way round: unfiltered fuel from the tank is supplied into the filter; excess fuel is going straight into the injection pump...unfiltered.
All fuel coming from the return line passes through the filter and is filtered prior to returning to the tank.
My expertise ends here; one would have to measure whether flow rates are affected or whether you still get the required amount of fuel through that setup.
I venture out and suggest that the injection oump receives sufficient fuel with the filter mounted "backwards" because the fuel supply to the injection pump is not restricted by any filtering.
I had to go outside and look at my own filter! The mickey mouse clip and thermo tee sit on the side facing the engine.
Now...that means that my filter is mounted correctly, right? RIGHT?
After three dealers having their fingers in my engine bay, I would not be prepared to accept ANY responsibility as to whether that filter was in correctly or not. Who knows who put it in the wrong way round, provided it ever WAS in the wrong way round.
Voiding your warranty based on that seems a bit hefty.