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So apart from clearing junk, restricting spawn point to the one closest to the last position of the player will help a lot. The use of cryo tubes might be considered, but they have always had issues and may refuse to work in some situations resulting in being unable to spawn and requiring admin help or somebody to go grind the cryo. Also if you have meteors enabled or are doing massive planet mining operations the planet data files can grow enormously which is obviously another potential problem. ... so take a good look at the server save, and see what you can clean out of it, either using the standard ingame or server UI admin tools or with SE Toolbox. (obviously take a copy first in case of errors)
The old version on Steam is not, but a new programmer took it on and his version is updated whenever SE updates, you can download it from their github page - https://github.com/mmusu3/SEToolbox/releases
You can also use the ingame admin tool to clear craters - alt-F10 > trash removal > Voxels
And that trash removal doesn't clear craters worth a crap. O_o
:) yeah, sorry about that, at the time I typed that I was in a real bad mood after being awake for almost 36 hours apart from the couple of hours I spent in a coma on the floor... I think you need to consider sharing more detail, like any mods in use, as the in-game voxel reset tool should never fail once you get to grips with the usual terrible Keen user interface, and I've never seen toolbox fail to open a save unless there were whierd game-altering mods in use.
Alternatively you could upload the server world save to Steam and share it so I could investigate (hidden/passworded if need be)