I see, I just thought it odd that it doesn't touch my start.bat file or save files, but does delete the server_settings.json file. Like I said in the original post I figured it out and solved it for my own use case by moving the files outside of the install as you said.

A update command would be ...

"I am on Windows 10 using the installer from factorio.com/download"

I login to factorio.com/download and use the "download space age for windows" button. I then extract the files from the .zip folder and run the Setup_FactorioSpaceAge_* Version_Number *.exe file. The game install is updated to the ...

Every time I update Factorio Space Age using the setup file my server settings file is deleted causing the server to fail to load. I have always kept my server-settings.json in the factorio/data folder in the install with the server-settings.example file. I just moved my start.bat and server ...