Your thread title 'Section numbering screwed up' implies something to do with Section breaks & headers, for which I took your reference to heading 3 not continuing on from heading 2 to be a reference to header content, not to the Styles named 'Heading 2' & 'Heading 3'. It would be easier to provide help if you expressed the problem with greater clarity.

If you start by defining the Heading Style multi-level relationships with 'Heading 1', working through all required Heading Styles systematically, all of the Style deinitions will be updated automatically without the need to select anything other than the initial paragraph with the 'Heading 1' Style. Furthermore, there will be no room for any of them to go awry part-way through your document unless someone has overridden the Style-based formatting with hard formatting at some point. Even then, however, it is only the overridden paragraphs that will be affected.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]