Farting in the truck will likely void the warranty, so... Unless they can prove the bypass filter directly contributed to the failure, they can't legally deny coverage. That's not to say they'll not start by denying coverage. If the fails in any way that could be caused by lubrucation, you'll likely have a hard time getting them to change their mind since the bypass filter "alters" the factory lubrication system. The fact that it makes it better will probably not be relevant. If the high pressure fuel pump fails, you.sgould be able to get them to cover it since the lubrication system has nothing to do with the fuel system.
Bottom line is expect to fight for coverage if altering anything.
Bottom line is expect to fight for coverage if altering anything.