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If you're going from FLVs (especially Sorenson Spark codec) back to FLVs you can't help but lose quality. Depending on the original bitrate, the loss of quality can be very apparent. FLV VP6 codec is a bit better, so the results may not be as bad.
You'll get the best results if you can go back to the masters used to create these clips.
If you can stand not to have the watermark added throughout, you can join FLVs without encoding. You can put the site name in the pre and post rolls. Adding the watermark will however require a re-encode.
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