Arduino Uno upload danger question

Am I in danger of destroying the built-in bootloader in my Arduino Uno? I would like to experiment with trying to write a c or asm program using AtmelStudio6 to produce a .hex file and then to upload it into my Arduino Uno using AVRDude. However, I wish to then be able to go back to loading the regular type .ino programs using the standard Arduino IDE. Will I mess things up if I attempt the above?

Will I mess things up if I attempt the above?

Yes if you use the same memory space as the bootloader which is at the top (high memory addresses) of the memory. This occupies the op 2K so keep clear of that.

If you erase all memory you might get rid of the bootloader. But you can use the same process to put it back. The bootloader .hex file (or files) are supplied with the IDE.