Dear Sinead,
thanks for the interesting question and welcome to the ROOT community!
I think that this kind of subtraction makes sense only if you match the gen information to the reconstructed one - this is something that can happen in many ways, and has to be coded in a matcher by you - this is not generic enough to be done for all use cases by RDF. Nevertheless, you have all the pieces at disposal, for example in the VecOps namespace.
The end result should be a list of reconstructed tracks (basically you have that already) and a list of matched gen truth, adapted to match that recoed info.
I hope this helps!
Cheers,
D