I solved.
Apparently it seems to occur when only the .exe file is overwritten at the time of update.
After downloading the new version of the server, I solved it by migrating in such a way that only user-specific data was applied to the new server.
I hope it will be useful information for you.
Sorry for my poor English.
Same thing happened to me.
I really hope for a solution.
I'm Japanese. sorry if my words are weird.
To @v-weszaj
The PS4 platform I checked did not experience the same phenomenon in single player worlds.
I'm guessing that it probably only happens on dedicated servers.
We may have to wait for information on other platforms.