After, completing a document assembly request, if Pathagoras detects a Table of Contents,some end notes and/or other cross-references in the document, Pathagoras will ask if you want to update those links in the following message:
You will typically say yes by clicking the Update button, but you could delay the process by clicking the red X.
You can avoid the question altogether, and tell Pathagoras to update cross-references automatically. To turn off the ask, go to the Document Assembly tab in the All Settings screen, ("Pathagoras Features | All Settings' (the purple button). Check the 'Auto-update cross-references' box. (Beginning with Pathagoras 2017, the box is pre-checked.)