There are a couple options:

1.   You could do it yourself.  There are several examples with code in this foundry project (ogg for example).
2.  You could contract QNX to do this through custom engineering.  We would add it, and then provide you a patch against
 our commercial product and it would be tested and supported by us.
3.  We can wait until it is included in an upcoming release.  At this point there aren't plans for flac support.

We're happy to help you best effort with #1.  You can email me (dcardamore@qnx.com) if you choose to go #2.

Dan