As a person who studies metaphysics, how might I deal with the logically proven fact that we live in a dream/simulation?

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Metaphysics doesn’t depend on any particular fact, whether it’s true or false or silly or illogical. If it turned out that the Flying Spaghetti Monster were real, it wouldn’t change metaphysics at all.

Metaphysics is non-empirical, you don’t study it by doing experiments and making measurements. You do it by thinking really deeply about the concept of existence and what it means.

The relationship between mind and matter doesn’t change if we’re in a simulation. It doesn’t change in your actual dreams. The nature of experience is exactly the same. The nature of change isn’t any different. You can’t step into the same real river twice, and you can’t step in the same simulated river twice.

Metaphysics arises out of the fact that there are things that are of the world that have the capacity to reason about that world. No amount of intuition about how matter operates makes any difference.