Hi Dishant,
See if this helps.
The function module used for outbound idoc is "IDOC_OUTPUT_DELVRY". There is a custom exit available ZXTRKU02 (EXIT_SAPLV56K_002). In that exit, see if you can modify the 'idoc_data' which has all the segments of that IDOC. Before adding the code, just write a break-point statement and see if the data you are looking is present in the IDOC_DATA structure. If it is present, then try to write a code to delete the line item (E1EDL24).
Let me know if it works.
Thanks,
Sandy