You’ve put content in template’s header, when you update document from template, it will place content from template’s header to document being updated. It’s expected behavior.
Do this in your template:
File → Properties → Custom properties. Click add Property. Name variable ‘DocNum’, choose Number from the drop down, enter ‘1’ in the Value input box.
Now go Insert → Fields → More fields → choose DocNum under Custom. Click Insert.
Now all you need to do in any of your other documents is define ‘DocNum’ under File → Properties → Custom properties. Just place there a number you would like to use with that particular document and everything should work on template update.
But don’t put in template any content that’s specific to one document and you wouldn’t want new template update reverts it. Insetead ‘Document 005 NewDocName’, template should have only ‘Document 005’ and five being a filed that changes dynamically.
You could even in new documents set document title: File → Properties → Description → Title and enter title for that particular document there.
Then insert title filed in your template after: Insert → Filed → Title.
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