No, acquiring an artifact due to an encounter (such as Discover Treasure) does not restrict the player from performing the Recover Artifact action at that location later, even if the artifact color matches one already collected.

Explanation

• On page 31, it states:
  "You can still only take the 'Recover Artifact' action on Artifacts that do not match any of the Artifact Token colors in your collection. If you happen to draw a random Artifact of a color you’ve already recovered, that does not violate the rules."

This means:

• The restriction on the Recover Artifact action applies only to that specific action, not to artifacts gained through encounters.
• If you gain an artifact of a color you already have via an encounter, it does not prevent you from later using the Recover Artifact action at that location, as long as the artifact token at that location is of a color you do not already have from the Recover Artifact action.

Source: page 31.

Source: Core Rulebook (pp. 12, 14, 20, 26, 31)