If you can identify exactly which .mcr files you want to delete, you should be able to delete them with no damage done to the rest of the map. Once someone else ventures out there (when you increase the border range), it will simply generate those chunks like they were before, as if it was the first time the chunks were getting generated (using the same seed and all).
You seem to have uncommented some lines that should have remained as comments. "Uncomment to enable mod" actually refers to the line below it ("modCheatEnabled = yes").
Every time there's a blank line, the first line afterwards is a brief description of what the option does and so should remain as a comment.
So, for example, the first couple of lines originally look like this:
# Uncomment to enable mod:
#modCheatEnabled = yes
You changed it so it looks like this:
Uncomment to enable mod:
modCheatEnabled = yes
But it should actually look like this:
# Uncomment to enable mod:
modCheatEnabled = yes
The "modCheatEnabled" line should be the ONLY line you remove a '#' from in the Cheat Mod section of the config. I noticed that several other options (presumably all the options you changed) have been uncommented in the same way. "Toggles Cheat mode on / off", "Show / hide ores", "See through everything nearby..." and all the other lines that look like descriptions should still be commented with a '#' sign in front of them. It's the lines below those comments ("keyCheatShowOres = C", "keyCheatSee = T", etc.) that actually do anything.
Best Answer
Your selector,
@e[type=!minecraft:bat]includes a!, which inverts the selection. In this case, the kill command killed every entity that was not a bat, when you really wanted@e[type=minecraft:bat]. Unfortunately, unless you have a backup, there's no real way to recover from this as far as I know.