Dan, they most likely didn't tell you all the facts during your 744 conversion as the philosophy is "need to know" for pilots. Only the flight engineers delved deeper into the intricacies of systems, alas no more F/Es to enlighten you on the 744. However on the question of HEPA filters and how often they are replaced by maintenance, see the following.
Myth: When the air filters get dirty, they're no longer effective.
Fact: The high efficiency filter, in particular, actually becomes more effective because the trapped particles make it more difficult for other matter to pass through. The filters are replaced at regular maintenance intervals. If several intervals were missed, and an abnormally heavy build-up of particles occurred, the only effect would be reduced flow of the recirculated air -- but whatever air did pass through would be extremely well filtered. In any case, the filters do not affect the flow of the outside-air portion.
So my advice, please keep those recirc fans on, as it says in VOL.3