I have not written any logic to have the sequence EKKO, EKPO, EKPO, ESUH, ESUH in the cenverted Step, rather I am just assigning the Qty value (from PO Item Source File) in the Limit fields under ESUH Segment and PACKNO ('Number' variable from Function Module in EKPO Segment). LSMW is automatically building that sequence in Cenverion Step.
As specified earlier even providing separate Source load files for ESUH and ESKL does not solve the purpose as those do not have the PACKNO value in it and since the sequence of standard LSMW Segments executions is EKKO, EKPO, EKPO,... ESUH, ESUH...., ESKL, ESKL...., therefore always the last PACKNO populated in the "Number" variable in Functional Module (in EKPO Segment) is assigned to all the Line Items of ESUH and ESKL Segments.
I think storing PACKNO values in internal table is the only solution in this case.