This issue still persists, although I do not think anyone is losing any AP, not any you should be having anyway.
After noticing of "losing" 2AP, after doing Kaineng Meta, I did some testing, and what I believe is the issue, that some repeatable achievements, that also have Tiers with AP, give more AP than they should under certain circumstances. Essentially, the Tiers still add AP, even if the achievement is already at max AP. So for example, if the "Eternal Seitung Province Meta-Event" is at max AP, and Tier 0/3 it will give exactly 3 AP total, if it is at Tier 1/3, it will give 4 AP (3 + 1 from Tier) and at Tier 2/3, it will give 5AP. The extra AP from Tiers only get added after a map change tho, and only show up on the total AP, not on the achievement itself.
The reason why some people appear to have lost some AP, is that once the Achievement is completed, it will reset back to Tier 0/3, and not give any extra AP from the Tiers, thus removing the incorrectly added AP. (again, only visible after Map change)
To reproduce:
Let's say you have 1000 AP and the "Eternal Seitung Province Meta-Event" is at max AP (3/3) and Tier 0/3.
Complete the Seitung Province Meta and swap map, you will notice you now have 1001 AP.
Completing it again, and swapping map, will result in 1002 AP.
Once you complete it a third time, the achievement will go back to Tier 0/3, and AP will reset back to 1000.
It seems like the re-calculating of AP on loading, does not respect the max AP an repeatable Achievement should be able to give, when it has multiple Tiers that give AP.
I hope this helps narrowing down the issue.