Yeah, this is what is says...
Please note that if your file contained any of these commands that we specify separately, they were removed:
I personally find it to be easier to just have everything in this one txt file. It makes managing things like the server names easier. Just copy-paste from one server's Startup.txt to the other and simply adjust everything from there.
Also, I adjusted vars.vehicleSpawnDelay
recently in the Startup.txt but rather than reading it in from that after a restart, it seems to have read it from the Easy Setup so I was confused for a while why my server had started up at vars.vehicleSpawnDelay
50 rather than vars.vehicleSpawnDelay