In answering your first question, it is probably caused by where your cursor is when adding the new entry.

CrossRefs to an automatic paragraph number point at the number on the FIRST paragraph inside that bookmark. If you put your cursor in front of that heading (where the bookmark includes the full heading) and press Enter to insert the new paragraph then the bookmark EXPANDS to include both the new and old headings (and the first paragraph is not the one you intended the bookmark to point at).

To avoid this behaviour when inserting content in front of numbered items put your cursor at the end of the paragraph above and insert the new paragraph there (and apply the style it if necessary)

To address question 2 I would need to see sample documents because I don't fully understand what you are currently doing. I think it is likely that Charles' suggestion (on the other forum) to use Content Controls is going to be part of the solution.

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Andrew Lockton
Chrysalis Design, Melbourne Australia