The most logical thing is not to select it in the first place
Code:
Sub TestMacro()
Dim shp As Shape, aRng As Range
For Each shp In ActiveDocument.Sections(1).Headers(wdHeaderFooterPrimary).Shapes
If shp.Type = msoTextBox Then
Set aRng = shp.TextFrame.TextRange
aRng.MoveStart Unit:=wdCharacter, Count:=1
aRng.Font.Subscript = True
End If
Next
End Sub