The microcontroller Flash (128 kB) contains both the uploaded program and the bootloader. The bootloader is a small program which is executed at the beginning and proceeds to run the uploaded program. Libelium provides the Waspmote IDE which will not permit rewriting the bootloader.
Do NOT use other IDEs, only the Waspmote IDE is recommended.
If the bootloader is overwritten by using any of the previous practices, the warranty will be voided.