If you pass 'generate' to the mkconf script, it attempts to parse some
existing values out of the file, then does an "exec >$CONFIG".  At this
point, the output file has been removed, and is effectively 0 bytes in
size.  All the existing content is gone.

Later on, if there is an error, the script might abort writing the full
file out; this is because set -e is in place.

Please write to a temp file, and do an atomic move at the very end.