FedEx is going to get $10K (or whatever the amount required and paid is, it could be less) one way or the other at the end of the lease. Should the landlord determine that there is sufficient reason to keep the deposit, I would bet that the pilot is going to have to repay FedEx. I can't imagine any other way it working out based on the language of the FCIF.
Potential pitfalls? You bet.
Should you be concerned about this if you are going to an FDA? Of course not. $10K is not a "substantial" amount or enhancement.
FJ