Fast copy or full conversion
Later FLV files usually hold H.264 video with AAC or MP3 audio — the same streams a modern MP4 uses. Those can be copied straight into an MP4 container without touching the picture, which is quick and completely lossless. Older FLVs contain Sorenson Spark or VP6, neither of which any current device decodes, so those need a real re-encode. The tool works out which case your file falls into, and taking the copy path whenever it is available is always the better result.