Hey Alex311, it looks like the only issue was using TextRange.PasteSpecial (ppPasteRTF)... I used the regular paste and it worked like a charm.

Here's my updated version (tested and working flawlessly)

Sub switchNotes()
Dim oTarget As Presentation
Dim oSource As Presentation
Dim i As Integer
On Error Resume Next
Set oTarget = Presentations("target.pptx")
Set oSource = Presentations("source.pptx")
For i = 1 To oSource.Slides.Count
oSource.Slides(i).NotesPage.Shapes(2) _
.TextFrame.TextRange.Copy
oTarget.Slides(i).NotesPage.Shapes(2) _
.TextFrame.TextRange.Paste
Next i
End Sub

Hoping it can help you and others as well.