This question's been on my mind for quite some time now.
After the initial battle at the arena, R2-D2 reattaches 3PO's head. But the folks had already left:
So, who went back to retrieve these two?
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It would appear that Yoda's 'Clone Troopers' won a stunning victory on Geonosis. Not only did they destroy one of the Trade Federation's droid transports but they also managed to completely obliterate their droid factories.
Given that they'd won and had no need to leave the planet in a hurry, there's no special indication that they didn't simply double-back later to pick up the droids and mop up any further resistance.