Updating gamelists adds both .cue and .iso to gamelist file, thats why you get double entries.
nadenislamarre don't modify /recalbox/share_init/system/.emulationstation/es_systems.cfg
cp /recalbox/share_init/system/.emulationstation/es_systems.cfg /recalbox/share/system/.emulationstation/es_systems.cfg
then modify this new one.
And then ssh into recalbox and edit the copy of the file, removing .iso extension. (Incase you miss some games, just create a matching .cue file with needed data (use the data part from any existing .cue file as a template)