Well, here is a quick stab at the problem. It seems to do the subspace stuff that it needs to, though it does not remove shields from the ships when the transition happens. Patch is also included in the attached archive with an fs2_open_3_6_13d_INF_SSE build and pdb. Unfortunately I am unable to build FRED right now, so FRED will complain about the sexp not existing.
I haven't done a subspace mission for so long I don't remember if any of the effects are missing. Please try it and I will clean it up to apply to the 3_6_12 branch.
Removed code and link to build. See my next post in this thread.