I don't know.. it may be possible to trick Vdub by creating jobs with avisource() pointing at some other file. Then, after the jobs are created, point those avs files to where their respective huffyuv exports are supposed to end up.
This seems like the shortcut could take longer than the just doing it all in two passes. I'd just render out the unfiltered huffyuv files with jobs. Then, once those jobs are done exporting, I'd create new jobs with the filtered avisynth scripts and run those.
You could probably save yourself more time doing two things at once by busying yourself with fine tuning the avisynth scripts and filters while the unfiltered huffyuvs encoded.