I know you said you didn't want to do a bunch of format conversions, but let me ask, what format are the vids that you have in before they become FLV? (or did you get them as FLVs?) Can you go back to the app for the original format, trim and re-save? (for example, Final Cut or Premiere)? Then re-batch to FLV?
I guess it would depend on how many you need to do. Probably not practical if you need to edit a thousand vids.
(just thinking out loud here.)
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