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.