How do I convert a 24-bit/96 kHz FLAC to anything else?
Personally I use a tool called X Lossless Decoder, or XLD for short. I use it for converting FLAC to Apple Lossless regularly, and it’s never hiccupped.
From the project’s page:

XLD can decode following formats:

(Ogg) FLAC (.flac/.oga)
[…]


and:

XLD supports various output formats. It can convert audio files into […] MPEG-4 AAC (QuickTime/CoreAudio), MP3 (LAME), Apple Lossless, FLAC […].

XLD is free, and is still being actively maintained. Highly recommended.