Can you change the duration of a video in Handbrake? I have a 1h25m 25fps video file that has an audio file that is 1h29m. I want to change the duration of the video from 1h25m to 1h29m.  Is this possible with Handbrake?

I tried setting the duration to 1h29m up near frames/duration but Handbrake didn't change the video. I know how to change duration with Sony Vegas but I lose quality in the conversion, so I want to do this with Handbrake for higher quality.
Yes, you can select the desired length by chapters, time or even frames.
BUT this only works properly when Audio and Video have the same length (video is always cutted correctly, audio not).
So you have to either 
1. cut the audio track with Audacity or any DAW (Tracktion is really good and free) to the correct length and mux it back together afterwards (Yamb for MP4, MKVToolnix for MKV) or you can 
2.add a chapter mark at the end of your video and put the video into fre:ac (the best audio converter I know), check "encode to a single file" and unselect the last of the appearing titles (everything after your chapter mark). Now you can convert your audio into anything you want. fre:ac only detects mp4 chapters, you can edit/add them with Drax and you have to use fre:ac alpha version to use this feature.