I've noticed that if anything changes in the config file between updates that it seems to automatically create new variables however, it seems that this is a bit of a hit and miss as it sometimes can overwrite existing values that have been changed by the user

While this is nice it can lead to issues so here's a proposition; The event that any sort of changes are made, there should be some sort of method to keep track of the config version that gets updated whenever internal changes are made for the sole purpose of being able to inform the user on the first world the client joins (similar to the welcome back message) to inform them that The config Needs to be updated.

I'll be honest when I say, I'm not exactly sure how to go about this because what you're doing currently is certainly better than just rewriting the entire thing outright

To clarify: when I mean by overwrite existing values, I mean, it creates a new variable that has the change and have a higher priority in occurrence; this is the case when I found multiple different shader2 options in the config