(as @slhck suggests:)
FFMPEG can indeed remux FLVs into MKVs, regardless of the codecs used. But - this functionality is (relatively) recent, so:
- Make sure you have an up-to-date version of FFMPEG. If you don't, download one from the official site (you might be referred off-site for Windows builds).
- Run
X:\path\to\ffmpeg.exe -i input_file.flv -c copy output_file.mkv
And that should work.