If you want to generate negative commissions for your affiliates in Post Affiliate Pro you just need to enable ''Allow to compute negative commission'' option in the Merchant panel configuration.
You can find this option at Configuration > Tracking settings > Tracking levels
How does it work:
When this function is disabled and you are tracking negative transactions, all negative commissions will be set to zero commission instead.
When this function is enabled Post Affiliate Pro would compute negative commission instead of zero-based on your set up in Campaign > Campaign manager > Commission settings