Hi Rajesh,
Check event 120, which is used to allocate the clearing amount to the correct original item of a collective bill.
The table T_FKKCL_ALLOCATED contains the relevant line items to which the amount must be distributed.
You can plug in a custom FM, which will check for the disputed child invoice and will remove it from the above table so that the payment doesn't gets allocated to the child invoice.
Hope it helps...
Thanks,
Amlan