Hey, @Kolia_Nik.
As Gareth said, you should be very careful about what you do close to a server restart.
The server restarts happen every day by 10:00, 18:00 and 00:00 server time, as they have for many years. As a general rule of thumb, it’s a good idea to not do anything dangerous within 30 minutes of a restart.
Our logs are very limited in regard of these cases also, so unfortunately we can’t help you out here.
With that said, our guidelines also say the below:
And it looks to me like you modified it after being destroyed.
From what I can read in Discord, it sounds like you had problems with an invisible enemy. This is unfortunately a common bug in Empyrion, and isn’t related to the disconnects. This bug can unfortunately happen to anyone at any time, regardless of how far into the season we are 
So in the future to be able to help with something like this, a video would be great, and please don’t modify your structure.