I would recommend that if you want the macro to run correctly when
invisible, you avoid as far as possible the use of the following objects

- ActiveDocument
- Selection
- any Window object, including ActiveWindow

For the most part, you can avoid using the ActiveDocument, as follows. When
opening a document, using the following syntax

Dim oDoc As Document
Set oDoc = Documents.Open(FileName:=C:\test.doc")

After that, whenever you are in the habit of using ActiveDocument, you can
use oDoc instead.

Once you have a reference to oDoc, you can do the following to define a
range

Dim oRange as Range
Set oRange = oDoc.Range(0, 0)

Then you can do almost anything with oRange that you can do with Selection.
In addition, you can define as many Range objects as you want or need, and
use them all simultaneously. You can only have one Selection.

With regard to breaking the link between sections for the header and footer,
you don't need to use the Window objects or the Selection at all for this.
There are several ways to approach this but probably the simplest is as
follows. Assume that oRange is pointing to somewhere within the section
whose header and footer you want to unlink, proceed as follows

With oRange.Sections(1)
 .Headers(wdHeaderFooterPrimary).LinkToPrevious = False
 .Footers(wdHeaderFooterPrimary).LinkToPrevious = False
End With