From what I think when you convert something you sometimes lose quality... like a CD to MP3, or a paint drawing to a jpg.
The quality shouldn't change all that much.
If you are really wondering, if I were you I would just try getting a small 30 second FLV clip and convert it to MP4 and check the difference. If you are satisfied proceed to the full FLV.
I have a video in FLV format, and want to convert it to MP4. I'm wondering if any quality will be lost in the process and if it's worth it. Thanks