Just a question, did you added the files of the catalog inside the catalogsSE.pak, and then packing them again using a compression program like 7-zip? Because when you recompress that file sometimes it does in 64 bit zip version and SE seems to have problems loading again the catalogs from that file (It happened to me).
So, if that's you problem, NEVER RECOMPRESS THE OR EDIT THE PAK FILES. You don´t need to do that! Just copy the planets and stars folders with the .sc files inside them directly to the catalogs folder. Also you will need to get the original CatalogsSE.pak file again, reinstalling SE in another folder and just getting that file or restoring a secure copy if you did one.
If that's not your problem the only solution I can imagine is that you bad edited universe.cfg. Notice the method. You have to add the file inside planets folder also in config.cfg.
For example the file NeutronStarsMain_complex.sc inside the planets folder must be also added below "PlanetsCatalogs (" pointing where that file it is: "catalogs/planets/NeutronStarsMain_complex.sc". And the saving the file. If you have also a file in the stars folder you have to add it but in this case below the "StarsCatalogs (" line. So, as long you add lines and don´t delete any lines in universe.cfg there is no point that the solar system dissappear. If the line "catalogs/planets/SolarSys.sc" is still there SE must be able to load it.
My work for SE: Click here Textures for Venus surface in color and the moons of Saturn, Uranus and Neptune Catalogs of binary stars, brown dwarfs, black holes and neutron stars.