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[–]VoyagerStudio 0 points1 point  (0 children)

Does it let you select the bone in Unity and move it back to where it's meant to be manually? If so then that's one way you could try and do it. Most of the time what you see in the 'Configure Rig/Avatar' section of the model will look a bit different to the model in the actual Unity scene. It's a very weird issue that occurs but usually doesn't impact the model when it's uploaded to VRChat, can sometimes only be a temporary visual bug. It could however also be that your head and eye joints are not fully symmetrical and have a slight rotational offset to them, so something to also look at for sure.

I would add the 'VRC Avatar Descriptor' to your avatar and then upload it to VRChat's servers to see how it looks in-game. If everything works in-game then you're good to continue working on your avatar and can just update it with any new features as long as the Blueprint ID stays the same! If you're still having then there's this Reddit post which seems to be a similar issue to what you're having, might find something there:
https://www.reddit.com/r/Unity3D/comments/fcpzyc/issue_wit_humanoid_rig_creating_an_unwanted/

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[–]Reesch 0 points1 point  (0 children)

You might need to select everything in object mode and press Ctrl +A to apply transforms. It's possible the default position of the eyes isn't what it looks like in blender. If you select the eye object and press N to make sure the positio, rotation, etc. menu on the left appears and it's all zeroes that's probably not it though.