To convert from [.flv] to another format, use VLC Media Player’s [Media > Convert/Save] option. Be sure to set the destination as well as the source. VLC can only convert to formats in its own internal container and codec sets, but e.g. can convert to [.mp4] containing H264.
Thereafter can use e.g. Sony Vegas to generate e.g. [.avi] containing CFHD, e.g. for onward use in applications that don’t recognize mp4-h264. Vegas is more accommodating and flexible than (straight use of) Adobe Media Encoder, as regards non (broadcast) standard frame sizes and proportions. Conveniently, Vegas automatically matches the Project to the footage on footage-import.
Prior to that, I tried installing and using Riga, the two-way FLV convertor, but it didn’t work on my Window 7 (64-bit) machine, opening only a blank window where a GUI was expected, and both the downloader and installer were both full of bloatware (NB needed to install in Advanced mode in order to avoid some of that). Pointless…