Solved!
Correct, you can use the bootloader with a .hex created by mikroC PRO, no problems there. The problem was in addressing the USART. The Axon/ATmega640 addresses the USART's as USART0, USART1, USART2 and USART3, as to mikroC PRO's USART1, USART2, USART3 and USART4. Using the USART1 on the Axon for communication with the PC must be addressed as USART2 in mikroC PRO.