Simey, I have had an opportunity to look at the changes, and can fix my issue easily, as you suggested, by changing the path to the base flowplayer .swf files. It would also be easy to add the same usage pattern to the other .swf files located in the filter/rtmp directory except for the hard-coding of the directory name in lib/flowplayer/lib.php (line 55). I think it would be better to not assume the only .swf files used in the application are in that one directory.
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filter_rtmp broken by Flowplayer changes
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