DO you want this to happen when GR based inv verification is enabled?
do you debit the transporter for the loss? if you do that then have a debit note debiting the transport vendor and crediting the material vendor. this way 99 from will come from GR and 1 will come from debit note in FBL1n.
if you dont debit the tpt vendor, see whether you can adopt the same by debiting a dummy vendor. check with your FI team