Scouring the interwebs, I found some methods of converting from FLAC to m4a if you don't mind using the command-line in Terminal. With both options make sure Homebrew is installed which is a package manager that will allow you to install the requisite tool.
Using ffmpeg
Make sure ffmpeg is installed (google Homebrew to install) and type:
ffmpeg -i [infile].flac -acodec alac [outfile].m4a
(There are a few shell script gists on Github named flac2alac which use ffmpeg and will preserve tags: https://gist.github.com/)
Using flac and afconvert
Make sure flac is installed (google Homebrew to install) and type:
flac -s -d --force-aiff-format -o [tempfile].aiff [infile].flac
afconvert -f m4af -d alac [tempfile].aiff [outfile].m4a
(This shell script gist was helpful: https://gist.github.com/mlen/4379799)
This will convert to a temporary loss-less aiff file, then using Apple's command-line utility afconvert, to loss-less m4a. You can then delete the temporary aiff file.
The limitation of this approach is that the temporary aiff file generated has a maximum capacity of 2GB, which one of my files would have exceeded. So I needed to use another approach for this file.
Using flac only
I was also able to convert directly from FLAC to m4a using flac only, but the resulting files were twice as large. It seems flac doesn't apply any compression, whereas afconvert and ffmpeg compress the resulting files.
Regards,
D.