Is there a way to route an output from HS2 or HSSE2 to an audio input to record so that I have a separate wave file?
I want to export to ProTools or WaveLab for mixing and mastering.

there are a lot of ways … My preferred way
Use VST connections to make a dummy bus(s). Route your VSTi outputs to the dummy busses. Route the dummy busses to audio tracks.

If you are just making stems to take to pro tools, just use the export functions.

Thank you very much for the info. It is much needed.