Your post makes no sense,gog updated with no messages and after that when i loaded no mans sky there was no save file to load,rm the file?What does that mean?
The save files you think are missing are located here:
With RM Button I mean Right Mouse Button.
Go look if your missing files are still in the DefaultUser folder (look at the date), if yes, no problem: start the game as usual. If no, do as I suggest above to solve your problem. This may not work however, it depends on the restore settings in Windows, how often restore points are created and how much GB you assign for it. If this doesn't work, I'm afraid your files are lost.