I have to ask *why* you would ever want to encode right from dvd with HB, then re-encode again with VH ? Trust me when I tell you that you are taking way longer than you need to and getting *very* lossy video.
May I suggest one of two workflows depending on what software you prefer:
1. HandBrake straight off the dvd to final movie (realize some newer dvd's with advanced protection may need to be pre-ripped with mtr or fairmount/dtox first ).
2. rip movie with mtr or fairmount and then encode with VH.
The workflow you are describing is not only very long, but you are getting lossy conversion in each step, so your final quality would be much lower than a one encode process.