Can a manufacturer / trader raise a separate invoice for freight of goods for b2b trade?

One of our b2b customer wants us to send material to their warehouse by road which will take 5-6 trips by Tata ace.
They want us to bill for material separately (one invoice per trip ) and a separate bill for total freight cost ( all trips) . Is it OK under GST ?
If so what HSN code will freight fall under? My customer has suggested an HSN code 996511 ( nil GST ) whereas my product falls under 18%