Hey Thijs!You can first convert your wav files to 44.1k oder 48k with sox:
currently i can convert the most common formats, but i'm having trouble
converting 32bit/96kHz stereo wav files : flac and oggenc dont like them :-(
i have tried with ffmpeg and various settings but i cant get it to work
$ sox your_96k_file.wav -r 48000 your_48k_file.wav