Which file are you having problems with? Is it Batwoman - 1X01? If that's the file, there's a problem with the frame rate. The file is marked as constant frame rate at 29.92, but probably should be 29.97. Eventually this can lead to dropped frames or stalling on output.
Funny thing. I did that exact routine, open wtv direct with VideoReDo, last evening and it worked perfectly. I did change up to a constant of 29.97, in Handbrake, and the result file was very small as I hoped. I wonder if I could rerun several files thru Handbrake with these changes and then load VideoReDo. Would VDR6 find them acceptable? Your thoughts?
There is an easier way to do this. Well two actually...
1) Open the original WTV file in VideoReDo, make your edits, save to a Force Recode profile that emulates the same settings you're using in Handbrake. Resulting file is both edited and recoded in one pass.
2) Open the original WTV in VideoReDo, make your edits, save to a Smart profile. This should be fast. Open resulting file in Handbrake and recode that instead.
This was VideoReDo is working with the original file instead of the recoded one, which should help save quality and incompatibility.