If I place the insertion cursor next to the paragraph end mark where the section break resides, the Style toolbar on the Ribbon says “Heading 1”. If I then press the Del key, the section break is removed. If I go back to the same paragraph end mark, the Style toolbar on the Ribbon says “Normal”. The style of that paragraph got changed automatically by removing the section break on its own. I might be wrong but I see a link between the style of that paragraph and the “associated” section break.

We are off on a tangent here.

1. This has nothing to do with the problem presented. Changing which style is applied does not change the TOC or the numbering or the order of entries.
2. If instead of pressing delete, you apply the Normal style, nothing changes for the problem.
3. A section break, any kind of section break, can never be part of a Style's definition. A paragraph format setting of Page-Break-Before can, but we are not seeing that here.

Back to the original question/problem:

1. Kilroy identified the problem - different methods for applying numbering
2. I suggested using Shauna Kelly's method of attaching numbering to styles and using the styles to set the numbering.