well, flv is already high compressed so is there any reason you need to transcode?
regarding your audio issue, you can use I think Goldwave (pc only) to stretch or shrink the audio, only if your audio is progressively out of sync. If your audio is consistently out of sync (e.g. always 2 secs ahead) you can shift it in many softwares by putting a positive (delay) or negative (earlier) millisecond value.
another alternative is to leave the audio as the original (if it is aac, don't bother re-encoding), select "pass-through" or "Copy" for the audio track