Based on your attachment, the following macro should be enough to repair the footnotes and their references. That said, your attachment seems to have other issues as well. For example, the body text has the 'Header' Style applied, but that's been completely overwritten with a different set of formatting.
Code:
Sub RepairFootnotes()
Application.ScreenUpdating = False
Dim FtNt As Footnote, Rng As Range
With ActiveDocument
Application.OrganizerCopy Source:=.AttachedTemplate.FullName, _
Destination:=.FullName, Name:=.Styles(wdStyleFootnoteReference).NameLocal, Object:=wdOrganizerObjectStyles
Application.OrganizerCopy Source:=.AttachedTemplate.FullName, _
Destination:=.FullName, Name:=.Styles(wdStyleFootnoteText).NameLocal, Object:=wdOrganizerObjectStyles
For Each FtNt In .Footnotes
With FtNt
With .Reference
Set Rng = .Duplicate
Rng.Collapse wdCollapseStart
Do While .Characters.Last.Next.Style <> wdStyleFootnoteReference
Rng.FormattedText = .Characters.Last.Next.FormattedText
Rng.Collapse wdCollapseEnd
.Characters.Last.Next.Text = ""
Loop
.Characters.Last.Next.Text = ""
FtNt.Reference.Style = wdStyleFootnoteReference
End With
With .Range
.Style = wdStyleFootnoteText
.Font.Reset
.ParagraphFormat.Reset
.Characters.First.Style = wdStyleFootnoteReference
End With
End With
Next
End With
Application.ScreenUpdating = True
End Sub
For PC macro installation & usage instructions, see:
Installing Macros
For Mac macro installation & usage instructions, see:
Word:mac - Install a Macro