I have had 1 COD shortage in my career. I collected a check for exactly $10. under the amount owed. I went to the business the next day, he wrote me a check for $10, I tried to enter it into the board with the sheet that UPS gave me and it would not go in. That night, when I got to the center, I explained to the center manager and my driver supe what I did and showed them that the check did not show in my end of day.
I wanted to make sure that my butt was covered for when someone said that there was still a discrepancy.
Sure enough, 2 or 3 weeks later, the boss called me into the office to ask about it. I reminded him of the envelope and the fact that I could not scan it and all that. He called security or whomever and that was the last that I heard of it.
The key with a discrepancy is once you do collect it, make sure that a manager sees that it is collected.