So it looks like its trying to establish a hyperlink to the first
file, rather than fixing the hyperlink of the old one. I can change
the cell contents to match the filenames on en mass if this helps.

OK, so that was a hyperlink you previously fixed.
I assumed you hadn't fixed any of them.
Try this:

Sub ChangeHype()
Dim WS As Worksheet
Dim H As Hyperlink
For Each WS In ActiveWorkbook.Worksheets
For Each H In WS.Hyperlinks
' change it to start after the last \
If InStr(H.Address,"\")0 Then
Debug.Print H.Address
H.Address = Mid(H.Address,InStrRev(H.Address,"\"))
End If
Next
Next
End Sub

Bill Manville
MVP - Microsoft Excel, Oxford, England
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