According to this thread: https://github.com/KeenSoftwareHouse/SpaceEngineers/issues/158 The disappearance of ships is linked to world size and anything over 20Km is subject to the bug even with jump drives disabled. The post concluded setting the world to infinite eliminates the the bug. I was under the impression however that the server was configured for infinite world? If that is the case, the bug is unique and other solutions should be looked into.
If the issue is regarding the cluster split error ( issue #158 the error gillgamesh mentioned) then it appears that welders can also cause the split error and that currently the only way to fix the error would be to remove the world border.
I was told by Thodd to reset the world YET AGAIN over the weekend due to this bug. I backed up the world file in case we wanted to revert back to the previous one. We removed the world border on the last map and it was still happening so Thodd suggested we do a map reset with a zero world border from the start to see if it would stop it from happening.