Akwat Kbrana said:

Ok, I see where you're going with that, but it begs the question: why? What possible reason could Sidious have for issuing such an order?

Well perhaps once he has the chancellorship, the droids are useless to him? Just thinking out loud here. In fact, if we went with the idea that Dooku is a maverick jedi and NOT a sith led around at the nose by Siddy, then this "betrayal" of the viceroy would fit right in with Dooku's discussion with kenobi in AOTC about the viceroy coming to Dooku about this dark lord's betrayal.

Sets up the next movie and the motives of the viceroy for giving Dooku, in our cut a well-intentioned good guy, the federation resources to fight the republic.