In conclusion it's all about the mind at work here and how you go about using a VR headset, making sure you don't get used by the headset itself lol.
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That is probably your experience, may I give you a harmless experiment for your eyes?
Try this. Don't try to focus or unfocus your eyes, neither of the two. Just let the eyes be, be alert about the image projected in your conscious.
Keep focus on the whole "image", all of it at once. This is not a use of the eye muscles and nerves to focus on something, no. Drop those, and try to see everything at once. Once you get that, you will feel like your whole reality has become one, instead of individual reality per eye movement.
Now with this, your eyes will always be intelligent when it comes to meeting with "dangerous screens". Please try it. Remember, don't focus, just notice, or in other words, just "check", be as delicate as you can with this process. If there is even a little tension, then you are doing it wrong and using focus again, either focusing or unfocusing.
You will know it worked if you see in a new way for the first time, also try not to scoff before experimenting, hopefully you try it.
Oh, PS. This is not to be tried with VR, I'm talking irl. Try VR once you get this mastered if you catch my drift somehow.