The general rule for spell effects is that unless the spell says that saving vs. or suffering an effect grants a lingering protection, it doesn't. (It's not that common.)
Control undead (and by extension the Command Undead feat, which is based on control undead) does not have such text. This means that you can indeed keep re-casting it until you run out of channel energy uses or break the target's will.
Provided it's not higher HD than your level, that is...