If you don’t already have sox installed, do this to install it:

$ sudo apt-get install sox

Then run this to do the conversion, in the folder with music in:

$ mkdir resampled
$ for flac in *.flac; do sox -S "${flac}" -r 44100 -b 16 ./resampled/"${flac}"; done

And that’s it - it will convert all the .flac files in that folder to 16 bit at 44100 kHz and put the result into the ./resampled subfolder, preserving the metadata.