Hi Marc,
Air in the System is unlikely to be the cause here, though if it has been drained, I would strongly recommend having the System evacuated under Vacuum to be sure there is no Air as this is what causes rusting inside the System that can lead to failures of the interconnecting pipe work and the hoses to the bags.
A number of items can be the cause, and it's suggested that they are all checked;-
Worn Knuckle Joints,
Mis-match between Bags,
Sagged Bags (and this is the likely cause),
Wrong Upper Front Arms (Dry instead of Wet),
Wrong Rear Helper Springs,
Wrong Rear Struts
Probably what's not always realised with Hydro is that just like the Dry set up, it does sag over time, but usually takes longer. While Front and Rear bags are different when new, you'll likely find by now the characteristics between them are about the same, so swapping Fronts to Rear is a viable option. To check for this, leave the Front end on a Jack, front wheels in the air, for 3 - 4 weeks (or longer if you can), be sure to leave the Rear on the Ground during this time. This will to a small degree let the Fronts come back a bit. If when you do put it back on the Ground, and roll it around a bit, you find the Front is up, then that's the likely problem.
You can also fit some spacers (washers) between the Front Bag and the Knuckle Joint, however you are limited to a total of 0.150" of Spacers (which theoretically will Raise the Front by ~3/4"). The factory express Warning against fitting any more than a total of 0.150" of spacers here as it can break the socket inside the bag. Having said that, there are late Knuckles which already have a spacer included and you can add 0.150" safely to these as the Pin is still the standard length, so engagement will be OK.