Other Fuel System Fuel Injection System problems of the 2009 BMW 535

The car suddenly displayed a warning saying the fuel pump malfunction and gave a notice that engine may shutdown immediately and to pull to a side. We complied - though it may have been pretty dangerous if we were on highways or in traffic. Tried to start again, the same issue. Got it toed to the BMW dealership. The dealer diagnosed the issue to be the high pressure injection pump and told us it is not covered. We called BMW and they told it is now covered as it has an extended warranty. We tell the dealer and the dealer tells us it is covered but another part edk pf is now not covered as it did show fault codes that were earlier than the fuel pump fault codes. My issue is if the fuel pump and edk work hand-in-hand, won't the two to be covered by BMW? why it should matter, which did show fault codes first? infact this is pretty dangerous situation and I wish BMW recalls and checks all vehicles and fix all the parts that are affected.