Willy

Thanks to some helpful folks at r/handbrake, I was informed that if you enable Detelecine, Interlace Detection, and Deinterlace, and then set your frame rate options to "Same As Source / Variable Framerate" then ideally your mixed media source video will be properly deinterlaced all the way through. Handbrake will intelligently detect what parts are telecined and what parts are standard interlaced and deinterlace each accordingly. This does produce an output file with wildly varying framerates (24 to 40-ish fps in my testing) but the result runs smooth as butter in all scenarios I've witnessed, with much less bloat than deinterlacing to 59.94p. So that will likely be the method I'll use for DS9 and Voyager - with the Deinterlacer set to Decomb with EEDI2, since that produces the best quality results.