Secret areas stuck at 26/32

I know where every secret area is, and whenever I go the 6 final ones, it displays a message saying I found them. I check my collections, and everything's great, 32/32 secret areas found. But whenever I save and load my game, it goes back to being 26/32, and it lets me "find" these 6 problem areas again.

Anyone with this problem, and do you know how to fix it?
 
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