put your lv2diag.self and ps3updat.pup on the root of the usb and use the port closest to the blu ray drive. it should begin the downgrade, it seems to me that the console is in factory service mode.
if you formatted the hard drive or even if its one from a different console or if you tried swapping some important files in dev_flash it will not actually boot into factory service mode where you can see anything on screen it will just turn off. and if you have already tried this use a different usb.
the CORE_OS.PKG which is found in a playstation update pup is stored in the consoles nor or nand chips, so whenever you update the system this is wrote to the actual chip, so yeah, not all firmware data is stored on the hard drive. e3 flasher or progskeet type drvies lets to reprogram this.