Atlas map not found in the atlas

Solution 1:

The only way to get maps that do not appear on your atlas are non-map sources such as Zana's shop, delve and seemingly metamorphs. While in maps, the only eligible drops are the maps at the exact tier shown on the atlas screen.

To progress the atlas (i.e. spawn the conquerors), you will need to run maps at the tier they are shown at on the atlas while you have the minimum amount of watchstones socketed in the correct region.

Dig is a T11 map base, meaning that's when it first appears, which I believe is at 3 stones in its region. If you run that map with 1, 2 or 4 watchstones, it will not be eligible to spawn conquerors. It will not appear at 1 or 2 stones, and would be the wrong tier at 4 stones (you would need the T14 dig at that point).

Map completion progression/bonus objective should be unaffected as it doesn't care about watchstones, only that you kill the boss and map rarity/corruption.