After Pathagoras completes the assembly of the document and completes the processing of an <<*Options/Optional/Repeat*. . . .>> blocks, it will scan the document for the presence of any Tables and Lists (Table of Contents, Table of Authorities, Bibliography, List of Figures and Illustrations, Indexes, etc.) It will also reattach Cross-references to their precedent reference and restore any links to the Internet (URLs and Mailto: references) that were temporarily unlinked during processing.
You can turn off the automatic updating of these references in Utilities/Settings | All Settings | Document Assembly. Look for the Post-Assembly section (upper left).
The 'Tables' and 'Lists' to which we refer above are those that are part of, and found behind, Word's 'References' tab. Pathagoras offers an addition table, that being Table of Abbreviations and Acronyms. This is a non-Word tool that tells Pathagoras to locate what it thinks are abbreviations and acronyms and their expansions. To be 'seen', an abbreviation or acronym must be in ALLCAPS, be less then 8 characters in length and be immediately followed by it expansion with an opening and closing parenthesis. E.g., ADA (Americans with Disabilities Act), NYT (New York Times), VBA (Virginia Bar Association).