Why does user program like Blink.ino.mega.hex trash the bootloader.

Development Tools IDE 1.x
1

I had to erase and reprogram my Arduino Mega2560 R3 memory with Atmel studio 7 and AVRISP mkII. When I use the hex-file with bootloader, for example Blink.ino.with_bootloader.mega.hex, Arduino IDE works. But after that, if I burn a hex-file without bootloader like Blink.ino.mega.hex, the IDE stops working. IDE says timeout from AVRdude.
Isn't there addresses in hex-files, why does an user program like Blink.ino.mega.hex trash the bootloader.

Blink.ino.mega.zip (10.7 KB)

2

ISP programming deletes all the flash including the bootloader. use Burn bootloader and then disconnect the programmer and use the USB upload

3

Yes. I noticed that AS 7 erases the chip as a default. Is it possible to use IDE to upload hex-files?

4

LMI1:
Yes. I noticed that AS 7 erases the chip as a default. Is it possible to use IDE to upload hex-files?

other then normal upload over bootloader?
there is "Upload using programmer" in Sketch menu