@wsamh There is some hidden key to ignore some systems.
Just add:
<system>.ignore=1
at the end of your recalbox.conf, reboot and that's all.
<system>
being the short system's name. For example:
snes.ignore=1
c64.ignore=1
Short names are pretty easy to guess, but the full list of short names is available in the file /recalbox/share_init/system/.emulationstation/systemlist.xml
in name="..."
attributes of system
nodes.