Downloaded the save, nothing seems different after about an hour in single player mode (I teleport my character to Muluna and just sat idle there). Gonna try leaving the save running in multiplayer mode overnight, see if anything changes by morning.
I probably should have asked for some more specifics regarding "disappearing" nauvis, i.e. Can ships still travel to where nauvis used to be? Are the ships that were parked in the orbit of nauvis still accessible and viewable? Can you travel by starship to the place where nauvis was? Can you drop from starship into nauvis? Is it just the icon itself that becomes invisible?
Are the routes to nauvis still accessible and viewable? Can you check the properties of nauvis in the Factoripedia? Is nauvis still available on the list of available Surfaces in the list when in the starmap view mode? Are there ever any players on nauvis when this disappearing event occurs? Can you try using the below command to teleport to nauvis, or does it fail for some reason?
/c game.player.teleport({0,0}, 'nauvis')
And just to confirm, you were not using the Nauvis Implosion mod at any point before this occurred? Only after nauvis disappeared, did you enable Nauvis Implosion to (temporarily) bring it back?
And finally, can you provide an image of the starmap when this occurs? That would really help answer most of the above questions. You can upload screenshots to imgur and link them here
Oh, and one minor note, Omnia is a ticking time bomb that you may want to remove from this save; if you research all technologies, such as by attempting to activate /cheat mode or just using the command, Omnia throws an error and sends you back to the main menu; this is an incompatibility with Planetaris Unbounded: Arig, as far as I can tell, (and the Omnia dev hasn't fixed it after two weeks of being initially reported) so if you want to keep Arig (and Planetaris Unbounded: Hyarion, by extension) mod, you will have to drop Omnia (idk what research causes the bug to happen)