The eboot.bin that updates the game executable is in the USRDIR patch folder, I think. The update came with 2 eboot.bins, one that is the root of the patch folder (that I think is respossible for placing the files in the correct places, i.e. updating) and another inside USRDIR. I tested this using Red Dead Redemption and I'm not sure if it fully updated, but something updated. The option for the undead nightmare appeared in the menu and it wasn't there before, in the 1.0 version.
Hmmm looks like not all updates have that eboot.bin in the patch root dir... Interesting.