Given that,
A body isn't necessary for resurrection.
Also, given that,
It seems possible for a PC to be killed, resurrected into a new body and then fight his reanimated corpse.
Is there any reason in Pathfinder or DnD canon why this shouldn't happen? I can always fall back to "He's a wizard and he used magic", but wondered if there were any headaches with this situation as a GM?
The description for Resurrection includes "You can resurrect someone killed by a death effect or someone who has been turned into an undead creature and then destroyed." (emphasis mine) That indicates to me that a) you cannot resurrect someone who has been turned undead until that undead creature has been destroyed and b) that it is possible to resurrect them once that has happened. This phrase is repeated verbatim on True Resurrection, so I'd say that no, this is not possible on a strict reading of the rules. Well, not without time travel, at any rate...
According to the spells' descriptions, resurrection does require at least "some small portion" of the deceased body. True resurrection is capable of "bringing back someone whose body is destroyed," so long as you have the correct information. In no case will raise dead, resurrection, or true resurrection make a second body – it either restores and makes whole the one you have, or creates a new one for you if you lack one.
In the situation you posit, there is a resurrected PC and what was his corpse in the hands of an antagonistic necromancer. The problems arise from under-specification of Resurrection and True Resurrection and where the new body springs into existence. The simple reading is that the magic creates a new body for the dead character's soul to inhabit within touch range of the spell-caster.
At this point, the corpse is just dead matter waiting to rot. Create Undead and Animate Dead simply require a corpse to target, so the necromancer has a valid target for all kinds of shenanigans.
There is one limitation I would place on this. The necromancer can't create an intelligent undead with the original PCs memories because the soul has moved on to another body. He could create an intelligent undead using the soul of another being. An entity from the Negative Energy plane or a demon with a strange sense of humour are both good options.
After this bizarre circumstance, the two characters are entirely different. While they may look the same, they are likely to act very differently.
As far as canon goes, nothing in True Resurrection says it doesn't create a second body, and you're the GM, so that's all you need (and you don't even need that, really).
As far as headaches, in theory a player might argue that you are violating the rules, and how dare you? But I don't think that's likely from what you say about your group.
Violating suspension of disbelief has been mentioned as a possible problem as well, but if true resurrection and creation of undead doesn't bother your player's sense of disbelief in the first place, I think that if the combination of the two does then that's just a little too idiosyncratic for you to be expected to predict it in advance. I would see this as more of a demonstration of the strange possibilities allowed by magic, and a sign that you have a world deep enough to have an internal consistency that doesn't match that of the real world.
If the body created by True Resurrection is destroyed and lost, the undead created out of the original body is destroyed and recovered by the player characters, and they try to use a Resurrection, then you may have another question to post :)
I wouldn't let an idea that you think your players might like be squashed by undue squeamishness about violating a rather grey area of the rules.
As said before, the resurrection spells can't duplicate a body. You may, however, want to look into the various magical abilities that do let you duplicate a body. Whether the PCs must be compliant in this act or not is debatable, so be careful if there are any rules-lawyers in your group.
Alchemical Simalcrum (and friends)
This list is hardly exhaustive, just what I could find that met the criteria with a quick search. There's also the option of creating a golem and shaping it to look like one of the PCs. In the same way, Create Undead and then Seeming to make it look like a PC.
There is also always Wish and Miracle, which can duplicate any of these spells. It's really up to personal preference; and remember, you always have the option of just saying "a wizard did it".
Is there any reason why the undead need to be the corpse of the fallen PC?
Since the idea of Fleshwarping exists, you can combine your necromancy spells + fleshwarping and you will be left with a undead that looks like the PC.
I'm just piping in to say that I love the concept, especially when you're talking about high level stuff like Resurrection and True Resurrection.
I think the Resurrection case is clearly precluded by the PC also being undead. But in the case of True Resurrection, I could imagine that a clone effect could be in effect. I mean, that's also the level of the Wish spell. So maybe you need to combine the two?
I know how difficult it can be to challenge high level characters, sometimes they are their own best enemy. So if it's good for the story, I would go with it.
Special thing to consider: Who gets the gear? At 15th level, that gear is very important.
As many people have pointed out, the resurrection/animation rules don't technically support this.
That said, holy crap that would make for an awesome encounter! Remember that the rules are only there to make an entertaining experience for everyone involved. If you can make a necromancer enemy more scary, and an encounter have more emotional impact by ignoring some of the fiddly bits of how resurrection and animation work, then go for it. Unless your players are super into the fiction of the Pathfinder world (assuming you're even in the Pathfinder world), I can't see any problems with allowing this.
You're the GM, aren't you?
The Necromancer learned how to clone the corpse, so even if the body was resurected, there's an undead, soulless copy out there. It's a shame the secret of this arcane power will die with the Necromancer.
