I'l be using the ArduinoISP sketch on an arduino uno to program an fpga throught SPI, but i want to be sure that i wont brick my arduino. Where is the uploaded bootloader saved between the serial comunication and the SPI? For what I understand it's in the flash memory.
The bootloader is just passed through the board used as an "Arduino as ISP" one page at a time. So it's only ever stored in RAM on the "Arduino as ISP" board.