The picture that you sent is caused by the incorrect uploading of files and does not have anything to do with the things that you mentioned.
I'm not really sure what issue you're having here because it seems like you have solved them yourself?
The bot does not ignore the second server in the config, but the config is made to support 1 to infinite servers, so it's possible just to delete the second server form the config and you won't have an issue.
If you want to fix the undefined when the server goes offline, within the single server, put something that says "SERVER_OFFLINE_MESSAGE": "[ OFFLINE ]" that will fix your issue.
To explain that a little better, you can just put it right after it asks for the bot token.
"RCON_IP": "",
"RCON_PORT": 28016,
"RCON_PASS": "",
"BOT_TOKEN": "",,
"SERVER_OFFLINE_MESSAGE": "[ OFFLINE ]",