I had this issue a couple weeks ago and posted in the pluspoints thread:
https://www.flyertalk.com/forum/36211662-post713.html

Ultimately I did have to call to get the points applied. I also spent a silly amount of time trying to get it to work, including getting the ticket revalidated, getting it reissued, actually changing flights, contacting web support, and nothing would fix it. I don't think there's any way to make it work again if it stops working on a particular reservation.