It would certainly be possible, but it would be a little weird to add this case because of an odd decision made in an unrelated device's unrelated firmware that seems to be based around the NERO encoder using .fla instead of .flac for some reason.
If I were you I would probably just keep everything in .flac, and keep a .bat file on the Cowon that renamed the newly added content and simply run this each time I transferred some media to the device.
Something along the lines of:
for /r "< DIR >" %%x in (*.flac) do ren "%%x" *.fla
should do what you want. Saved at the top level of the storage directory you would want parsed, this would do a recursive rename of all .flac files to .fla
[Saint]