I'm working on a dread necromancer and was thinking of fun things to do. I got the idea of having polymorph cast on undead I've raised. The question is, would the polymorphed undead still be under my control?
Well, if you are talking ordinary Polymorph...
According to the SRD, the target for Polymorph is one
Willing living creature touched
Undead aren't living, so they aren't a valid target for ordinary Polymorph.
Baleful Polymorph is also out, because Undead possess
Immunity to any effect that requires a Fortitude save (unless the effect also works on objects or is harmless).
and Baleful Polymorph only targets creatures and requires a Fortitude save.
This leaves us with only Polymorph any Object as a valid spell to polymorph an undead.
This spell is a true change. It alters something entirely into something else, including overwriting their mental scores and features. As Polymorph any Object otherwise works like Polymorph, it has the following effect as well...
The subject’s creature type and subtype (if any) change to match the new form.
This is a complete and total change of the target creature or object. They are not an 'undead shapeshifted to be a monkey.' They are actually a monkey for as long as the spell lasts. They get the monkey's mental stats, physical stats...and they act like a monkey, because they are a monkey.
At this point, we do not have a hard ruling that I can find, but I think it is a fair assumption that whatever you are dealing with isn't Undead anymore (it has lost the Undead type)...and thus cannot be controlled with Command Undead. So, I would rule that an Undead PaO'd into something not undead is broken free from the necromancer's control.
...but it is extremely poorly defined.
The general rule at play here is that the control effect of animate dead is instantaneous. It is not an ongoing spell effect, and can't be suppressed by e.g. antimagic fields. Unless something acts to change the situation (like casting more animate deads), the generic state of things you create is that "The undead you create remain under your control indefinitely."
If you squint at it though, you could read the control as only applying to "undead you create." Just like polymorphing them to e.g. a humanoid removes the undead immunity to cold, you could argue that the former zombies are no longer "undead you created"-ed with animate dead. They were previously, and the effect probably stays ongoing, but an effect which explicitly affects one thing has no effects on something else, even if that effect can be applied.
If you took the second interpretation, you would probably regain control as soon as they turned back into undead.
Further, if you took the second interpretation, the undead wouldn't suddenly become a full-fledged humanoid (or whatever). It would retain its no intelligence ability score.
A creature with no Intelligence score is mindless, an automaton operating on simple instincts or programmed instructions. It has immunity to mind-affecting effects (charms, compulsions, phantasms, patterns, and morale effects) and automatically fails Intelligence checks.
So, with that interpretation, it starts behaving however an uncontrolled undead behaves. Which is also completely undefined.