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1. Every single image is a standalone post. If you want to replace an existing image with a better quality one (png, larger size, whatever) just upload the new one and mark the old one as the child of the new one (optionally tag it as duplicate if it's a direct duplicate).

2. No. Yes you have to repost. You can also use parent function to link the two together. See: howto:parent/child.

3. In your case it's because it's a "dakimakura" image. Yande.re automatically hides the original resolution image of "dakimakura" post, even if you're the uploader. The image still exists on the server, you just can't see it.