You could probably use a macro like the following in your master PowerPoint file, to both update & break the links, then save the updated file:
Code:
Sub Demo()
Dim Sld As Slide, Shp As Shape
With ActivePresentation
.UpdateLinks
On Error Resume Next
For Each Sld In .Slides
For Each Shp In Sld.Shapes
With Shp
.LinkFormat.BreakLink
End With
Next
Next
On Error GoTo 0
.SaveAs FileName:=Left(.FullName, InStrRev(.FullName, ".")) & _
Format(Now, "YYYYMMDD") & ".pptx", Fileformat:=ppSaveAsDefault
End With
End Sub
The above code saves the updated presentation file back to the same folder, with the date appended to the filename in YYYYMMDD format.