Thanks for checking. I guess I either have to try ,ore drastic measures with my game, or repair it again before I start my actual run for the challenge.
I have this exact same problem now, and this is how I manage to temporary fix mine, not sure if it will help someone.
If you start your file and achievement points is "not" zero:
1- close game
2- go to origin and repair game
3- start game again
When I have to stop playing, I write down how many achievement points I have on a paper.
When you ready to start playing the file again, I open it up and check my achievement points even before I start playing.
If it matches, play.
If it doesn't match (sometimes the game collect points from your other files too), I will do the 3 steps above.
It is very time consuming and annoying, but oh well.