Finished product receiving discrepancy from retail customer

We verify shipped finished product counts to our retail customers.

If and when there is a discrepancy of that received count from retail customer how does one account for the loss according to traceability and how is it documented properly? (This discrepancy would not be from damage or refusal). 

So you receive goods from a supplier with discrepancy? You contact them immediately. You should be recording qty received on your doc for traceability. Your PO/SO form has qty ordered and qty received, mark it accordingly.  

Finished product count discrepancy is not being received by us, the finished product is what is being shipped TO our customers and is what THEY receive and record as a count which is the discrepancy that needs to be reconciled and documented by us as loss, but not because of damage or refusal. 

Then first find out what's causing such discrepancies, worry about documentation later.