HandBrakeCLI --help lists the available audio encoders. If I unpack the source, ./configure --enable-fdk-aac, and make, I get fdk_aac as one of the audio encoders. Of course, it is downloading the contrib/ stuff and building its own fdk-aac. The HandBrakeCLI built using the gentoo ebuild does not have fdk_aac (and the gui ghb does not have as an option). I have USE fdk, and I see -lfdk-aac in the link lines. But stripping out the contrib stuff is breaking fdk for some reason.
Thanks for reporting, apologies for the slow response. I will have a look into it. Can you post a build log? and an example encode log?
It appears that HandBrake requires FFmpeg/Libav be built with the fdk USE flag enabled. https://forums.gentoo.org/viewtopic-t-1045980.html
BT is right. rebuilding ffmpeg with fdk USE flag enabled gives me the fdk_aac encode option. Should a virtual/ffmpeg[fdk] USE dependency be added to handbrake?
In the tree now.