After reading through all of this again, I think the answers to my original questions can be summed up by the following demonstration:

[VBA]Option Explicit
Sub SetUpExample()
Dim oDoc As Word.Document
Dim oRngStory As Word.Range
Dim lngJunk As Long
Set oDoc = Documents.Add
Stop
'Step through code and switch between code and document to follow the process.
Debug.Print oDoc.StoryRanges.Count
'A new document based on a clean normal template contains 1 storyrange. _
'If formatting marks are showing, the headers and footers will be empty (i.e., no visible paragraph mark.)
'This is because the header and footer ranges are not defined at this point.

oDoc.Sections.Add
Debug.Print oDoc.StoryRanges.Count
'Adding a section does no effect the storyrange collection. This step is used just for setup.
'Isolate section 2 header from section 1.
oDoc.Sections(2).Headers(wdHeaderFooterPrimary).LinkToPrevious = False
'Reference a header.
oDoc.Sections(2).Headers(wdHeaderFooterPrimary).Range.Text = "Section 2 Header text"
Debug.Print oDoc.StoryRanges.Count
'Simply referencing a header or footer defines and expands the storyrange collection to include the six header and footer storyranges.
For Each oRngStory In oDoc.StoryRanges
Debug.Print oRngStory.StoryType
Next oRngStory
'As Gerry stated, every range has at least one paragraph so defined, formally (empty) headers or footers will contain a paragraph mark.

'The following code similates a user clicking in the section one header (defined with a single paragraph and no text).
oDoc.ActiveWindow.View.SeekView = wdSeekCurrentPageHeader
oDoc.ActiveWindow.View.SeekView = wdSeekMainDocument

Debug.Print oDoc.StoryRanges.Count
'This action removes (kills) the six header and footer storyranges from the storyrange collection as the following illustrates!!
For Each oRngStory In oDoc.StoryRanges
Debug.Print oRngStory.StoryType
Next oRngStory
On Error GoTo Err_Handler
Err_ReEntry:
Set oRngStory = oDoc.StoryRanges(wdPrimaryHeaderStory)
Do Until oRngStory Is Nothing
Debug.Print oRngStory.Text
Set oRngStory = oRngStory.NextStoryRange
Loop
'Since we've reference the section 1 headers and created the range, we are left with empty paragraph marks. Remove them as demostrated above.
oDoc.ActiveWindow.View.SeekView = wdSeekCurrentPageHeader
oDoc.ActiveWindow.View.SeekView = wdSeekMainDocument
oDoc.Close wdDoNotSaveChanges
Exit Sub
Err_Handler:
'There is no wdPrimaryHeaderStory defined even though we can see the text in the section 2 header.
'As Jason has discovered, section 1 defines the 6 header/footer storyranges. To ensure they are defined all you need to do is reference them:
lngJunk = oDoc.Sections(1).Headers(1).Range.StoryType
Resume Err_ReEntry
End Sub
[/VBA]

I think one of the flaws in my earlier understanding was that lngJunk does "NOT" fix a skipped header/footer, rather is ensures the the 6 header/footer story ranges are in fact defined.

Jason and Gerry, thanks for your interest in this post and your comments.