Place a server.cfg config file in a directory DIFFERENT from the main server files.
Start the server with e.g. the following parameters:
"F:\games\steamapps\common\Arma 3\arma3server_x64.exe" cfg=C:\Arma3_server\basic.cfg -config=C:\Arma3_server\config.cfg
You can create another config.cfg in the same main server folder with different content to compare which file is being loaded