IT is better than the alternative, replacing the sub-floor in a few years, and mabey some bugs.
Unfortunately there is no easy solution for this issue. It is what keeps contractors busy.
Oh, and make sure your paper above the flashing laps over the new sill pan. Kind of like making sure your raincoat is not tucked into your pants...or you get wet all over again.
But when you finish, it should be good for another 50 years. Longer than the door will last.