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Fffmpeg can encode/decode to/from webm starting with ffmpeg (ffmpe >= 0.6).
If you convert FLV to MP4 (H264 + AAC) you will not loose quality, however the filesize will be usually bigger. You need the original files to convert to H264 + AAC (and you will get probably the same quality as the original at a lower filesize). You cant use copy.
Ffmpeg can encode a file to a special H264 + AAC that will work on iphone, ipad, android, blackberry (and probably more smart phones).
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