Synchronize does not work as a nature influence in XD.
The out-of-battle effects for moves like Synchronize were not featured in Ruby and Sapphire... which was when XD came out.
You're better off saving before the fight, catching the Shadow Pokemon, purifying it, checking it's nature and resetting again.
If I remember correctly you can't see the natures on Shadow Pokemon until you purify them... but I could be wrong.
In other words, it's a huge headache.
For future reference the nature is set when you encounter it.
So you can't soft reset before purifying either. x.x;