Could you try the following case?

Lets create an excel workbook name is dummy1.xls including the code:
Private Sub Workbook_Deactivate()
MsgBox "deactivate"
End Sub
Private Sub Workbook_Open()
MsgBox "OLD message"
End Sub

And another workbook (dummy2.xls) to change dummy1 subs:
Sub ChangeMacros()
Dim vbc As VBComponent, i As Long, j As Long, strProcName As String, strTemp
As String
Dim strMacroList As String
Dim File
'On Error Resume Next
File = "c:\dummy1.xls"
Workbooks.Open Filename:=File, UpdateLinks:=0, ReadOnly:=False
strMacroList = ""
For Each vbc In ActiveWorkbook.VBProject.VBComponents
If vbc.Type = vbext_ct_Document Or vbc.Type = vbext_ct_StdModule Then
With vbc.CodeModule
If vbc.CodeModule = "ThisWorkbook" Then
i = .CountOfLines
If i < 0 Then
.DeleteLines 1, i
End If
.InsertLines 100, _
"Private Sub Workbook_Open()" & Chr(13) & _
"msgbox ""NEW message""" & Chr(13) & _
"End Sub" & Chr(13)
End If
End With
End If
Next
ActiveWorkbook.Close True
End Sub

When I run ChangeMacros, excel is crashing. If I manually remove one of the
subs (open or deactivate) from dummy1 and try to run ChangeMacros" sub in
dummy2, it is running without any problem.

Thanks