Not exactly what you want, but this should get you started.
Sub DoStuff()
Dim rngTmp As Range
Dim rngCells As Range
Dim wsRecon As Worksheet
Set wsRecon = Worksheets("Recon")
wsRecon.Cells.Clear
wsRecon.Range("A1").Value = "Invoice #"
wsRecon.Range("B1").Value = "AR Invoices"
wsRecon.Range("C1").Value = "AP Invoices"
Worksheets("AR Invoices").UsedRange.Copy wsRecon.Range("A1").Offset(1, 0)
Worksheets("AP Invoices").UsedRange.Copy wsRecon.Range("A1").Offset(wsRecon.UsedRange.Rows.Count, 0)
wsRecon.UsedRange.RemoveDuplicates Columns:=Array(1), Header:=xlYes
Set rngCells = Application.Intersect(wsRecon.UsedRange, wsRecon.Range("A1").EntireColumn)
Set rngCells = rngCells.Offset(1, 0).Resize(rngCells.Rows.Count - 1, rngCells.Columns.Count)
For Each rngTmp In rngCells
rngTmp.Offset(0, 1).Value = Application.VLookup(rngTmp.Value, Worksheets("AR Invoices").UsedRange, 2, False)
If VBA.IsError(rngTmp.Offset(0, 1).Value) Then
rngTmp.Offset(0, 1).Value = "Missing"
End If
rngTmp.Offset(0, 2).Value = Application.VLookup(rngTmp.Value, Worksheets("AP Invoices").UsedRange, 2, False)
If VBA.IsError(rngTmp.Offset(0, 2).Value) Then
rngTmp.Offset(0, 2).Value = "Missing"
End If
If rngTmp.Offset(0, 1).Value = rngTmp.Offset(0, 2).Value Then
rngTmp.Offset(0, 3).Value = "Duplicate!"
End If
Next rngTmp
wsRecon.UsedRange.NumberFormat = "$#,##0.00"
rngCells.NumberFormat = "0"
End Sub