Appears to be resolved as of this morning, everything is back to normal.
I saw the same thing this morning, all of my milestones were severely regressed. Thought it was a server sync issue so I backed out of the game and re-started. Server re-sync all good, same issue, milestones showing far less being completed, some of them back to zero. Clicked the individual tabs, it shows the individual milestones as being complete (10/10, etc) but they box isn't greyed out. I was able to find one achievement, lightsaber kills in arcade, that seems to have completely regressed, 0/500, when I know I had all arcade challenges complete. I'll give it a couple of days to see if it resets itself normally, and do a complete console re-boot (XB1), which sometimes fixes stuff like this.
