Easy, just kidding. I'm sure one set of books reflects legitimate accounting practice. The other reflects Standard Accounting Practice (SAP) for Athletic Departments.
As an OT aside, I think it's ironic that a recognized expert Economist in finance related college athletics can't be used by either side in the above referenced lawsuit. One side doesn't like what he says. The other, the NCAA, doesn't want anyone to hear what he says.
It is indeed a problem mainly for the NCAA that they can't defend themselves. They can't even mention, for instance, debt financing for arenas and stadiums. UConn is pretty lucky with the Rent, Gampel, Shenkman, Burton, new basketball digs, all paid for with cash outside the university.
But, if UConn really wanted to ramp up athletics with creative financing, it could have taken the donations for all of these projects, dumped them into an athletic endowment fund, and then bonded the construction of facilities through the academic side, which would finance the debt.
In other words, sometimes when you see a great amount of donations in the coffers, it allows the academic side to go into debt. This happened in Oklahoma St with T Boone Pickens. Although he ostensibly donated 180m for the new stadium, the school planned to plow his donation into the AD, and then bond the stadium through the academic budget. When Pickens lost billions in the meltdown and he didn't pony up the promised cash, it was a little awkward.
UConn is doing this the semi-honest way. If it had dumped 230m from facilities donations into the athletic budget, the AD would have 10m a year extra, and it wouldn't need a 10m direct subsidy from the academic side. Instead, UConn would be servicing the loan on the new facilities from the academic side, and no would be the wiser. This is how you hide losses, and UConn parents wouldn't have cause to complain about student fee subsidies either. Instead, they'd suffer the same losses directly through tuition, but who would read through the academic budget to find the line item of $17m a year in loan servicing for facilities?