FLV MetaData Injector, from Buraks, is a command line tool that adds the required Meta Data at the header of FLV files. You can even save an xml version of the details so generated. There is a GUI tool to make life easier, it even even allows you to select a folder and run the tool on the whole folder containing many FLVs.
FLVTool2 is another command line FLV Metadata Injector tool. Unlike the one from Buraks, this lacks a GUI interface.
Both the tools being command-line based, they can be used on the server to manipulate FLVs using a Server Side Script.
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