I have just downloaded an update but it is not being marked as updated in https://flightsim.to/user/my-downloads unless I manually mark it as updated.

Updates not being marked as downloaded
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It will if you update the page.
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I refreshed the page. It was still saying I had an update.
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Sorry - first guesses from own stuffups is usually the first reason to ask. Now, did you, when you saw this update marking still showing, refresh the page - in Firefox there's an arrow trying to swallow its tail up below the bookmarks on my PC that will do that for you. If the update is still showing, and you have the download on your disk already, then it's time for a visit to the support page https://flightsim.to/support/create-ticket because your problem isn't one I have experienced, and thay are in the best place to help you.
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Sometimes it takes up to 10 minutes for the system to detect the update and also update in all lists. If you are sure you have downloaded an update but it still does not show up after 10 minutes, please contact https://flightsim.to/support/create-ticket as JohnG said.