If you then start a new game with a progression point beyond this quest. . .the Beacon of light will still be present in the Crypt of the Ancients. You can even go and pick it up just like in the quest.
The other Beacon is not present in Warriors Rest after you pick it up and complete the quest.
To recreate this yourself- start a new game with the starting point as Return to New Tristram / Talk to Tyreal the last tab in the Act I list. Then go to the Crypt of the Ancients in the Festering Woods.
You will see the Beacon of Light sitting on the perch.