Every single course achievement of mine was backfilled right at the first launch. When I look at my website profile, they all show as not complete, and then show my 9 hole or possibly coin room scores being used. In game, they all show as complete. I'm a PC player.
A few examples from the website:
Merion Masher LVL 5 30/57 (progress bar only 1/2 filled)
Olympic Club Obliterator 29/57 (progress bar only 1/2 filled)
Oakmont Dominator LVL 5 12/57 (progress bar only 1/4 filled)
St. Andrews Triumph LVL 5 9/57 (progress bar only 1/4 filled)
I've only ever had two hole in ones, but my achievements say I have 9/10. Since this last update my score history for the past month now only shows CTTH scores.