Yes and no. When the portal changes location, the path to the boss also changes, closing the passage and preventing you from reaching the boss. If you have already passed the part where the passage is blocked, you'll be able to reach the boss and kill it. Otherwise, you will have to go back and go to the place where the vortex is open.
The image below shows the places where the passage closes:
I didn't include the Ankrahmun map, as it is always possible to kill the boss there, regardless of whether the passage is open or not. Just access one of the vortices that leads to one of the internal bosses (Eradicator or Outburst), and exit through the vortex of the lever room. Doing this will take you to the area where you can access the Ankrahmun boss.