My suggestions on this to aff programs:
1. Take the time to work this into your terms and conditions so as not to surprize your hard-working affiliates and ruin a relationship
2. Set a level that you are comfortable with if you are not willing to take the knock
3. be open and honest about the situation if it does arise and offer a solution that is amiable
We do not carry negatives over as we will take the knock and have decided to write it off as a marketing expense – it can be huge at times – a number that is never published that can even throw a program into a loss so webmasters do need to be aware of the impact that negatives can have.
My 2c..