HELP server using sponge totally ignores ALL configurations files

I change values for different mods, restart the server, then the pc itself, regenerate the files, use an old backup, and NOTHING WORKS. I can’t plant more apricorns in Pixelmon, I can’t turn on the whitelist, NOTHING THAT CAN BE CONFIGURED WORKS.

That sounds more like your config files are write-only or something similar. It’s definitely not normal behavior for anything, as you should be able to tweak the whitelist live, even on a vanilla server.

Please respond with what OS this is running, what versions of Sponge/Forge, and what exact version of Java.

Windows 10
Java 8 update 144

spongeforge 1.12.2-2768-7.1.4
Plugins being used:
CarrotShop-1.18-S7.0 1.12.2
greifprevention-4.3.0.662 1.12.2
Nucleus 1.7.0-S7.1 1.12.2
PixelmonEconomyBridge 2.0.1 1.12.2
Pixelmoney 2.2.0 1.12.2
projectcore 7.0.0-0.2.1
projectworlds 7.1.0-0.12.2 1.12.2
TotalEconomy 1.8.1 1.12.2

Forge 1.12.2-14.23.5.2772
Mods being used:
CDM-0.4.1 1.12.2
CFM- 6.2.0 1.12.2
Pixelmon-6.3.4 1.12.2
placeableitems-3.3 1.12.2