In dealing with FLV files, it's really nice to have the meta data available for flash players and other uses of the files. Unfortunately, when you convert a file with FFmpeg, it doesn't add this data in. FLVTool2 is a Ruby tool that does exactly this. Though it requires having a running version of Ruby, it's straight forward to install.
I took the Media Mover EXIF module that Robin wrote and basically swapped out a few things to replace it the FLVTool2 processing. It's straight forward and integrates in with the rest of Media Mover quite well.
What needs to be built along side of this is a library which can provide some of the basic functionality of FLVTool- making the file meta data available for other uses seamlessly. It should be fairly straightforward to do this, and likely, another module for other people to utilize. For this first iteration though, it adds the meta data so flash players should correctly report playing time.
UPDATE: You can grab it from the Drupal module page: mm_flvtool2



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