I've used VirtualDub to remove small things in videos before, but it would seem it's not super compatible with .flv files.
Are there any good programs out there that can cut bits from .flv files? Say I have a 30 minute .flv, I want to remove the first 5 minutes and not have to reencode it or anything so the quality of the remaining video is still fine.
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FFMpeg will cut it but only at the nearest I-frame if you do not reencode the video. You might also want to look into the VirtualDub external encoder feature available on the 1.10.3 + versions. There are several script you can download along with the required encoders like x264, ffmpeg, and mp4box. It takes a little assist to get it set up but it handles MP4, FLV, MPG and other formats easily once its set up.
Just an extra thought...