the bootloader does only support only W5100 chip, therefore the program got stuck in the EnterBootLoader(); function.
Could you please modify the bootloader source code that it will work with W5500 chip?
Or provide the source files for the bootloader? Because I only found the header files net.h, Bootloader.h, BootloaderDebug.h, w5100_reg.h and source file net.cpp. I think there should at least be a Bootloader.cpp, but this file is not included in your ShieldBuddy Add-In package.
Here is the source code for the bootloader. Unzip this to the "C:\Hitex\AURduinoIDE\Eclipse\AurduinoMulticoreUser" where it will transfer the relevant source files. The interface to the W5100 is in NET.CPP.