Achievement duplicated on GOG page and not unlocking

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So, I've been playing a bit of Phantom Liberty, enough to have a few achievements but those didn't unlock. For example the one for saving the president, did that on first day but it's still locked and appear twice on the GOG page. Any way I can unlock those without repeating all I did so far?
 
If I remember some also encountered this issue on GOG (achievements which appear twice). Apparently solved by performing a clean-install of the game.
 
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