There are disc-shaped foam/rubber-like pads under the clamshell that contact (and hold secure) the folded top assembly when down, and apparently leave these corresponding circular marks where they contact the top material. How to remove, I can't say, but I would imagine if you looked at the cloth fibers closely (like, with with a microscope or magnification) they would be compressed in those areas and relatively "fluffed up" elsewhere.
If this is true, maybe some sort of gentle treatment could help them get "fluffed" back up and make the circular marks disappear. Sort of how you'd clean matted-down suede. (Although I must admit, I don't know off the top how one would clean matted-down suede, but I'd think google might have the answer?
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