Thank you for letting me know. Prefab overrides are admittedly a pain for variables and overrides because these are serialized in a list and therefore when a variable/override is remove at the start of the list, the rest of the variables/overrides change their index in that list. This is why when you remove one, the others after that one are marked overriden, while the others before that are not. With that said, this is something I will have to fix/handle anyway. The simple solution will be to disallow removals and only allow value changes for overrides, but I will try to handle both. I will look at this again within the coming week.
Thank you!
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