If I intend to encode a video for FLV format for progressive download via a player on a website (not youtube or vimeo), what would be the best suggestion? Should I follow the procedure with handbrake and then go to flash in Sorenson or...?
You should have no need to render FLV now. Adobe Flash Player has been able to play MPEG4 files for a long time and penetration of compatible versions is very close to 100%.
I agree with you there, but for this particular website, they're using some video gallery component for Joomla that is old, and I'm fairly certain it only takes FLV files.
Oh I see. Not a bad idea to go via Handbrake for the deinterlacing quality, if you need that, but if you do then keep the bitrate really high as you'll only be using the output as an intermediate (which means a low quality crf value in Handbrake). Or you could use the Yadif deinterlacing plugin for Vegas to get better deinterlacing than Vegas has natively and then frameserve to your flv encoder or render a lossless intermediate (e.g. Lagarith or UT Video Codec).
If you are passionate about the very best deinterlacing possible, and have time and patience on your hands to set it up, you could use QTGMC in AviSynth. See my guide here.
If you have Sorenson and it does flv then that sounds like a good plan. I used to do my flv renders with On2 Flix Pro, but it's pretty much gone now, I think, and it was expensive anyway. You could do the flv in one of Adobe's programs, if you have those. I have a feeling the free program Super could also do flv rendering, but from what I recall it has a bad reputation for invading your computer.
I've also been very happy with the quality of Microsoft Expression wmv encodes of interlaced material (although I think it might be just be leaving the video interlaced and triggering a bob deinterlace on WMP playback.). However it is doing it, it really looks good.