After the Codex was retrieved it was brought to the Aing-Tii homeworld and placed into the Embrace. As a part of his five year journey to study the Force, Jacen Solo came into contact with the Codex when participating in the Embrace.
In 43 ABY, Luke Skywalker held the Codex when he went through the Embrace. At this time his presence in the Force was magnified so much that the Lost Tribe of Sith was able to sense him.