Untested....but should work.
Dim lastrow as long
lastrow = range("D65000").end(xlup).Row
ActiveCell.FormulaR1C1 = _
"=IF(MONTH(RC[-1])>3,"" ""&YEAR(RC[-1])&""-""&RIGHT(YEAR(RC[-1])+1,2),"" ""&YEAR(RC[-1])-1&""-""&RIGHT(YEAR(RC[-1]),2))"
Selection.AutoFill Destination:=Range("E2:E" & lastrow)
'Selection.AutoFill Destination:=Range("E2:E"& lastrow)
Range("E2:E1344").Select
Only exception being are you sure your Autofill code is perfect...