Soot is not really set up to deal with this. It's main data structure is the Scene, in which it holds all classes it reasons about and the scene can only hold exactly one class instance per class name - there can be no two different versions.
Having said that, we have recently built an extension to Soot called Reviser (currently under submission): https://github.com/StevenArzt/reviser Reviser incrementally updates a program's inter-procedural control flow graph and the induced IFDS/IDE analysis information. To make this work, we had to poke around with Soot's class-loading mechanism quite a bit, though; this is far from trivial. If you are interested in the details please send a personal mail to Steven Arzt and myself.