Alright!
I searched around a bit and found a link to this,
[size=78%]http://www.rane.com/note109.html[/size], on Gearslutz.
It says something along the lines of that your signal will get a bit fucked up in the low end and your synth might break if you are unlucky. I doubt that the latter is whats going to happen but if you want to know for sure; send a mail to DSI support and ask them.
I'd suggest getting a cheap mixer instead. There are loads to be had for less than $100, both new and used, which is a lot less than a Prophet 12. I see can the appeal of not having any extra gear which you don't really use though.
Is expression pedal control of program volume an option? You'd lose the ability to use the expression pedals for the things but it's an easy solution otherwise.