i had some trouble with that aswell but it does work.

Bring all 3 artifacts to mastarba together with anubis. Bring the artifacts to the ground map.
Do it a few times they start to dissapear and when all 3 are gone you can upgrade anubis his flagship

Yeah my solution to this was to drop the eyes one at a time onto the mastarba land units.

from a mechanics point of view if this is deliberate then you're probably *supposed* to do it that way, sending them to a fortress world to protect them from being lost in battle

problem is tartarus is my fortress world when playing as anubis