Apologies for replying to my own post, but I ended up doing a batch convert. For those in the same boat here is what I did to convert all my mp4's to flv's.
I grabbed a copy of ffmpeg and stashed it in a folder "E:\HyperSpin\Media\MAME\Video\convert\ffmpeg"
I moved all my mp4 videos to "E:\HyperSpin\Media\MAME\Video\convert\mp4"
I created a folder to stash all the converted files: "E:\HyperSpin\Media\MAME\Video\convert\out"
Ran this from a command shell in the folder "E:\HyperSpin\Media\MAME\Video\convert\mp4":
for /r %f in (*.mp4) do (E:\HyperSpin\Media\MAME\Video\convert\ffmpeg\bin\ffmpeg.exe -i %~f -c:v flv -ar 22050 -q:v 10 E:\HyperSpin\Media\MAME\Video\convert\out\%~nf.flv)
ffmpeg on my Surface Pro 3 (core i5 ) takes about 4 seconds per file (on an external hard drive). 4,258 files to convert should take just under five hours. It look as if the IO on the external hard drive is the limiting factor. CPU seems to be hovering between 20% and 30%.
Using "q:v 10" is pretty poor quality, but I am hoping this is only an interim measure until I can figure out how to use the native mp4. If you want to bump up the quality I would suggest using a value of 4 or 5 for q:v