If I understand you correctly, you're saying a customer agreed to pay you for services (product and/or support), either through posted prices and a shrink-wrapped license or through a written contract, and then you provided those services, and then they didn't pay?

And you're asking whether it's "OK" that they didn't pay?

Of course it's not OK! Is there any business who could operate in that fashion?

The way it affects the customer relationship is you don't have a customer relationship. You have a situation where they are taking advantage of you. A relationship goes in two directions.