Yeah, off the top of my head I would just assume compressed air to remove dust, and making sure that when in use the bags are kept sanitary on pallets and not stacked in areas where they would accumulate dust or possible pest damage.
A more "validated" solution might be to put them in some sort of steam chamber where you could actually reach lethal temperatures (the PP should able able to handle these), but then you have the problem of them coming out wet which would encourage mold growth in the fibers, you'd need a drying system as well........
If it was safe to hold your product, then you emptied it and stored it in a clean protected area..that might just be your best bet. Otherwise I can't think of a cleaning method that would "undo" a contamination event. In the PET bottles industry it was common practice for many years to re-use cardboard slip-sheets between layers of bottles (direct contact) and actually ship them back to the supplier to use again, discarding them as they deteriorated, became dirty, or were obviously contaminated. The PMO has a "disintegration" standard count for paperstock of 250cfu/gram that might be helpful for a validation of the microbial load on the bags?