If you need to convert an APE file into a FLAC file then that is easy. It also turns out it is easy to split the APE file into different FLAC tracks using a CUE file.
Flacon is an audio file encoder that extracts individual tracks from one big audio file and separates them into different tracks. It can also convert them in the process.
Flacon is available for many Linux distributions and can be installed on Fedora 25 with an easy.
sudo dnf install flacon
To convert APE files you will need also to install mac from rpmfusion-nonfree in order to read the files.
sudo dnf install mac
Simply select the destination directory, the pattern you want your files to be renamed as, what format you want them converted to and whether you want to apply replaygain. Then convert. It takes a surprisingly small amount of time.