If you still have the factory gravity III ballast then the fill pump is separate from the drain pump. The drain pump for that bag is located near the fitting at the bottom rear of the center ballast bag. Check to see if that pump is running. There aren't any sprinkler valves or anything like that on the drain side of the factory ballast system so if it's not emptying then it's likely to be a failed or pump or wiring/switch/fuse.
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2007 Mobius LSV
Tow Vehicle 2003 F250 6.0 PSD