qaac -r 96000 --he input.flac -o output.m4a
qaac 2.64, CoreAudioToolbox 7.10.9.0

output.m4a
48000Hz -> 96000Hz
AAC-HE Encoder, CVBR 320kbps, Quality 96

ERROR: AudioConverterFillComplexBuffer(m_converter, staticInputDataProc, this, &npackets, abl, aspd): -50

LCなら問題無いかもしれんがHEの最終安定版は2.62だな