What you do is an abuse of Heading 3 (or on the contrary of Heading 1 and Heading 2).
The Heading n styles are made for a document hierarchical structure. Yours is not hierarchical because levels 1-2 do not cause a “structure-break” (similar to a page-break).
Consequently, don’t use Heading 1 and Heading 2 which are associated with the chapter numbering counter.
Create derived styles MyHeading 1 and MyHeading 2 from the original ones: in the style side pane, right-click on the Heading 1-2 names one after the other and New. Name the new style My Heading n (n=1-2). The new styles will have exactly the same formatting as Heading 1-2 but they are no longer associated with the chapter numbering counter. Go to the Outline & Numbering tab to give them a TOC level with the menu Outline level in section Outline. Push OK.
Restyle your previous heading 1-2 paragraphs with your custom styles.
Your Heading 3 numbering is now continuous. In fact, Heading 3 becomes your chapter level.
Deriving your custom styles from the original Heading 1-2 ensures that any change you apply to the original styles will also automatically be applied to your custom styles.
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