Chargebacks & Adjustments

I would love some expertise on a cash posting issue my team has been dealing with.  Let me first explain the problem by giving you an example of what we deal with on a pretty regular basis.

My cash poster gets a $100 check for COMPANY ABC.  The remittance information that came with the check shows that they are actaully paying for 50 invoices that are $100 each. The reason the check is for only $100 is because they are taking one single $4,900 deduction. The deduction has nothing to do with the invoices being paid. For example, the $4,900 deduction could be an allowance that they think they are entilted t or a post audit claim for an issue from 2 years ago. Who knows? In any case, for this example my cash poster does not want to allow