Crazy as this sounds, we always used BarCode module to import into the Lot Field. My recollection is that the hard coded imports included a Lot Field. You just have to format the input file accordingly. Layout for Physical Counts looks like this:
Transaction Type (hardcode - ""8"") 1, 1
Warehouse Number 2, 3
Item Code 5, 30
Quantity (########.0000) 35, 13
Lot/Serial Number (if applicable) 48, 15