I don't use KubeJS, never even heard of it.
But after doing what "Ugdhar" suggested earlier in this post with the "config/Mekanism/generator-storage.toml", I tried going into an individual save's serverconfig folder, and just deleting everything except the parcool folder (I have that mod installed.)
Then, a bit of loading and temporary freezing later, seems to have worked.
Even when quitting to menu and loading back in, or also when quitting to menu, exiting to desktop, and re-launching MC, choose a save and loading it.