paginate()

This method of the section object (see section) triggers pagination of the current section. The pagination process re-establishes page boundaries, updates page numbers and page counts, and reapplies Master Pages.
Depending on whether page numbering restarts in each section this may affect the page numbers in other sections as well (see Configuring page numbers).
When the pagination process has ended, the script resumes.

The 'current section' is always a Print section, since this method can only be used in Post Pagination Scripts, and Post Pagination Scripts only run on the Print context (see Post Pagination Scripts).
You only need to call merge.section.paginate() in a Post Pagination Script if the script has added or removed content to such an extent that the page boundaries need to be renewed.

For an example see: Creating a Table Of Contents.