From what I can tell, the "fuel tank" sequence was to occur just after Grievous murdered Shaak Ti in front of Anakin and Obi-Wan on The Invisible Hand. Once Grievous had impaled her from behind (minds out of the gutter!), loads of droids would converge on Anakin and Obi-Wan, who would then use their lightsabers to cut a hole in the floor (similar to what Anakin did with the elevator) and drop through to the next level.
The problem is that the next level was the fuel tanks and (in what seemed to me to be similar to the underwater kitchen scene in "Alien: Resurrection") at one point Anakin and Obi-Wan would have to swim through a deeper portion to get to the other side and escape. The SBDs would pursue them and one actually catches Obi-Wan for a moment before they are finally able to get out and make their way to the elevator where they are confronted by Droideks and so on and so forth.
I would assume that this was cut very early on or else there was one of those Gungan dryer shields between the tanks and the elevators because otherwise I can't begin to imagine how neither Ben nor Anakin are "wet" during any of the subsequent scenes on the ship.
There are photos of this sequence in the animatics phase in the "Making of ROTS" book by the way, if anyone wants to take a look.