The following macro should do the job. It is best to try it on a copy of the original document first:
Code:
Sub ConvertCustomFootnotesToAutoFootnotes()
'Macro created by Stefan Blom, MVP, May 2016
Dim ftText As String
Dim r As Range
Dim ftCount As Long
Dim i As Long
ftCount = ActiveDocument.Footnotes.Count
For i = ftCount To 1 Step -1
ftText = ActiveDocument.Footnotes(i).Range.Text
Set r = ActiveDocument.Footnotes(i).Reference.Duplicate
ActiveDocument.Footnotes(i).Delete
ActiveDocument.Footnotes.Add Range:=r, Text:=ftText
Next i
End Sub