The quadrupole magnets for the LHC upgrade to higher luminosity are jointly developed by CERN and US-LARP (LHC Accelerator Research Program). These Nb3Sn magnets will be protected against overheating after a quench by a combination of heaters bonded to the coil outer surface and CLIQ (Coupling-Loss Induced Quench) units. The first 4 meter long prototype magnet, called MQXFAP1, was tested at the Brookhaven National Laboratory in stand-alone configuration. The magnet training campaign, consisting of 18 quenches, was interrupted due to the development of a short circuit between one heater strip and the coil. During the campaign, different quench protection schemes were implemented, including heaters attached to outer and inner layers, one CLIQ unit, and the energy-extraction system. The configuration including outer-layer heaters and CLIQ achieved the fastest current discharge, hence the lowest hot-spot temperature. The electro-magnetic and thermal transients after a quench were simulated with the program STEAM-LEDET and found in good agreement.