Completed 15 atlases in the past month, this has happened to me all the time.
As you can see on this screenshot (on the right) I discovered 50/50 regions on Xa Frant
On the atlas I still have 49/50, only happening with the last region (It is fixable by syncing the atlas with the world again)
Not a native speaker.
atlases don’t get their regions revealed by sitting in your inventory or in your hand. You reveal regions on an atlas by holding the mouse button down or “syncing the atlas with the world again” as you’ve said.
You can actually make another atlas and sync it and it will put all your discovered regions into the atlas.
I’m guessing you had clicked to hold the atlas up before the 50th region but not after.
Is that right?
Yeah you need to “use” the atlas after discovering the 50th region; otherwise, it just stays at 49. You have discovered the 50th region, you just need to record it to the atlas after. 
