Sponge global.conf removing added lines every boot

What title says.

Am using the minecolonies mod & trying to add these lines:

# Per-mod overrides. Refer to the minecraft default mod for example.
    mods {
        minecolonies {
            defaults {
                misc=512
            }
            # If 'false', entity activation rules for this mod will be ignored and always tick.
            enabled=false
            entities {
                citizen=512
            }
        }
    }

but everytime I boot my sponge server these lines get removed automatically.

Not quite. Every time you stop your server these lines get removed automatically. The Sponge config can be modified from commands in-game, so it must save its config on shutdown. To force it to reload global.conf while running, use /sponge reload -g.