In the opening scenes of The Phantom Menace we see the Trade Federation blockade of Naboo which features a fleet of many capital ships. In the climactic battle at the end of the film there appears to be exactly one capital ship. Where did the others go? Is there a deleted or even unfilmed scene that explains this?
They went back into Trade Federation space, presumably.
A single battleship orbited the planet, all that remained of the Trade Federation blockade. Housed within was the control station responsible for directing the droid army that occupied Naboo. When Panaka wondered aloud at the absence of the other battleships, Qui-Gon pointed out rather dryly that you don’t need a blockade once you control the port.
Everyone grew tense as they neared Naboo, but when they came out of hyperspace at last, no Trade Federation ships hung between them and the planet. “The blockade is gone!” Captain Panaka said in surprise.
“The war’s over,” Obi-Wan said. “No need for it now.”
“I have one battleship on my scope,” Ric Olié said.
Obi-Wan glanced over and nodded. “The Droid Control Ship.”
Since the droids on the ground control all of the major loading docks and spaceports, there's nothing to blockade any more. The planet has been garrisoned and the fleet can leave.
This was also addressed by Pablo Hidalgo in Star Wars Insider #80
Q. I noticed in the beginning of Episode 1 that there are several Trade Federation ships blockading Naboo. Why does this number change from several down to one toward the end of the film?
PH: Several lines of dialogue were trimmed in the edit of Episode I, but can still be found in the Illustrated Screenplay published in 1999. Upon emerging from hyperspace over Naboo, Captain Panaka notes "The blockade's gone." Obi-Wan dryly add, "The war's over...no need for it now." Given that the Trade Federation had rounded all the Naboo citizenry into camps and was on the verge of signing a treaty to legitimize their occupation, the frugal Nute Gunray reassigned his costly blockade prematurely, thinking he was on the eve of victory.