The question isn't how to workaround this. I can even patch the server binary if necessary. The server already has configuration parameters for loading missions, mods, Battleye, profiles, and storage from different locations — everything is implemented except for one thing: loading keys. We're just a bit short of reaching the ideal solution!

BI, if you are really interested in fixing this problem, I think you know what to do.
If you want, write me an email, I will share my observations, it will not force you to change the whole system, it will just allow you to calculate the level of trust in the server.

https://steamcommunity.com/sharedfiles/filedetails/?id=2905487932
https://steamcommunity.com/sharedfiles/filedetails/?id=2731250878
These mods will definitely show the problem, cut down a tree or use a gas station, stop the server after a short time (so that the files are updated) and the files will be broken

I also encountered this problem, when writing json, it seems that line by line writing to the file occurs, but the file is not cleared before writing.

@MarioE I was recommended by @OfficialWardog to tag you.

If suddenly someone encounters the same problem and needs a temporary solution, I made such a ad-hoc

UPD:
Today this happened to all servers at once

UPD:
At the same time, in this frozen state, the Steam Query port continues to listen, while the game ports and RCON are no longer available

UPD: and again

also does not find files if something is installed after the glob template, for example: