This is actually plausible. There's really three options here, and this is one of the top two.
I already outlined option 1 earlier (2:06 meant waaay more than $50-$75K reduction of his appearance fee). Some idiot even poo-pooed this, which show's he's either 1) never been a professional athlete, 2) never been an agent or, 3) a doofus.
Option two is your suggestion about waiving it, knowing that it will help ensure that he comes back next year. If this is the case, strong possibility that JH wrote him an agreement that he'll tentatively commit to next year's boston for the same or better appearance, and they would forgo the reduction clause for this year.
option three is the one espoused by so many here who think rupp is given immunity from these clauses because he's just that good. News flash. NOBODY is "that good," if you truly think this, see the three sub-points in option 1. This applies to you. If a race is spending $100K-$200K on bringing you in, they are going to GUARANTEE they see some sort of return on their investment, or their going to claw back. Period. Even Usain Bolt gets these clauses.