You need to ensure only Section 1 is protected e.g.
Dim bProtected As Boolean
'Unprotect the file
If Not ActiveDocument.ProtectionType = wdNoProtection Then
bProtected = True
ActiveDocument.Unprotect Password:=""
End If
'Do stuff
'Reprotect the document.
If bProtected = True Then
ActiveDocument.Sections(1).ProtectedForForms = True
ActiveDocument.Sections(2).ProtectedForForms = False
ActiveDocument.Sections(3).ProtectedForForms = False
ActiveDocument.Protect _
Type:=wdAllowOnlyFormFields, _
NoReset:=True, _
Password:=""
End If