I guess most of your concerns derive of your lack of precise acknowledgment about my system. It is not a standard pump and tank system, where, yes, the pump drains more and more amps when filling the tank, due to the air inside raising pressure NOT MY CASE. As I fill the bag, the air escapes through a hose which has a one way valve, that valve prevents water to enter again when "blowing" the tank, maybe a few drops through the tiny hole in he hose, while more "gallons" are pumping out through the pump, this way making the sub emerge.
FILTER: yes, there is one, I made it, connected to the water intake, find it here (and tested running the sub on surface and dived through dirty waters one day at the pond):
http://www.youtube.com/watch?v=iQQ-EubPou0
"How does the bag empty if there is a line to the sea,water will be coming in that way?" Would you still feel worried about it after 5 hours floating without loosing 1mm of waterline? I mean, it didn't sit lower in the water after that time. To be honest, that was the first thing I tested because I had the same concern.
And please keep in mind that the bag IS NOT FLEXIBLE, I'd say, semi-rigid. It will not fill and take more water than its capacity.
I designed and built this small system to install it the my 1/144 Seawolf, I have just a 2.5" diameter inside the WTC.
I am working in another project: a 1/50 TR1700 of the Argentine Navy, but this is a totally different project: no room restrictions (roughly 3.7" inside the WTC), and the ballast system will be a geared pump, a closed (pressirised) tank and solenoid valves.
Regards