Clarification: Okay, I read the text for the feat and spell again, and noticed a point of difference. Protection from Evil's Second Effect states that the controlled creature immediately receives a saving throw only if one was allowed in the first place. Command Undead (Spell) does not allow for a saving throw from mindless undead, but does for intelligent undead. Command Undead (Feat) allows for a saving throw from both.
So, going by the presence or absence of saving throws, a necromancer does not lose control over undead created by Animate Dead and mindless undead controlled by Command Undead (Spell), but loses control over all intelligent undead and any mindless undead controlled through the Command Undead feat.