If they claim that there was a verbal agreement for a fee other than the one for which you billed them, it would be their burden of proof to show what the agreement was. In the absence of a written agreement the court would look to the conduct of the parties to determine their intent. Their payment of your fee prior to the time of the deduction would weaken their case. This would be especially true if they have a late payment history.

If you cashed the last check you received from them after they made the deduction, you have a problem though. They can argue that your acceptance of the reduced funds is an admission of their position. It could also give rise to a defense in contract law called "Accord and Satisfaction" (settlement). They could argue that you agreed to settle the case for less than the full amount you were owed. You should have returned the check, and demanded payment in full. Having cashed their check will not make it impossible for you to win at trial, but it will definitely make it more difficult.