No. You have to erase the flash before programming via ISP, which deletes the bootloader as well.Why have a bootloader at all if you are using ISP for programming?The bootloader is only needed for serial uploading via USB or FTDI.
I see, thanks! I actually use both. Some boards don't have FTDI header soldered yet, so I use ISP. I guess I can just make FTDI jig with pogo pins... FTDI uploads also much faster than via ISP...
Now, if you're hand flashing them, you could combine the hex files - a script could probably do this quite easily, HEX is an easy format.
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