As far as I understand the case is about what a customer donating to the ADA through the CVS system would reasonably expect to happen, vs. what happened. It doesn't matter what the agreement with the ADA is. What matters is what the customer would expect based on what CVS was presenting to them and what happened.
So, consider 2 scenarios:
1. CVS collects $1mm from its customers for the ADA donations. The customers' expectations would be that the ADA would get $11mm. $10mm for CVS's legally binding payment, and the $1mm they donated through CVS. So the customers are short $1mm, and CVS is short $10mm.
2. This suit is claiming that the ADA still receives $10mm. The customer is short $1mm, but CVS is only short $9mm.
Irrespective of what CVS's agreement with the ADA is it sounds like a reasonable person can legitimately claim that #2 led to a donation to CVS, and not the ADA, and so CVS's representation was fraudulent.
Of course, money is fungible, so this is likely hard to prove. But the case seems like a fairly reasonable one on the surface.