See my comments in-line...

HTH,
Bernie
MS Excel MVP

Thanks very much! After a few tweaks it is sorting out the data and
deleting the appropriate rows beautifully. There is still one small
problem however- when I try to delete the helper columns, for some
reason the rows do not delete (I still have the whole list). Also, the
"G" column does not really delete, but keeps its header and the entire
column is filled with #REF indicating some kind of formula error.

Sounds like you are deleting the wrong column - but try my suggestions and see what happens....

Here is the relevant portion of my modified macro:
With Workbooks(nwb).Worksheets(ws)
myRow = .UsedRange.Rows.Count
.Range("G1").Value = "Counter"
.Range("G2").Formula = "=IF(C2=C1,1+G1,0)"
.Range("G2").AutoFill
Destination:=Workbooks(nwb).Worksheets(ws).Range(" G2:G" & myRow)

.Range("H1").Value = "Keep/Delete"
.Range("H2").Formula = "=IF(G3G2,""Delete"",""Keep"")"
.Range("H2").AutoFill
Destination:=Workbooks(nwb).Worksheets(ws).Range(" H2:H" & myRow)


Try changing these two lines below:

.Range(.Cells(2, 8), .Cells(.UsedRange.Rows.Count, 8)).Copy
.Range(.Cells(2, 9), .Cells(.UsedRange.Rows.Count, 9)).PasteSpecial
Paste:=xlValues, _
SkipBlanks:=False, Transpose:=False

to:

.Range("G:H").Copy
.Range("G:H").PasteSpecial Paste:=xlValues

and sort on H rather than I:
key1:=Workbooks(nwb).Worksheets(ws).Range("H2"), _

.Cells.sort _
key1:=Workbooks(nwb).Worksheets(ws).Range("I2"), _
order1:=xlDescending, _
Key2:=NONE, _
Order2:=xlAscending, _
Header:=xlYes

And instead of filtering on H, try

Dim myF As Range

Set myF = Range("H:H").Find("Keep")
Range(myF, myF.End(xlDown)).EntireRow.Delete


Remove this.....
With .Range("I:I")
.AutoFilter Field:=1, Criteria1:="Keep"
.Cells(xlCellTypeVisible).EntireRow.Delete
End With

and try this for the column deletion:

.Range("G:H").Delete