I dunno, it's quite possible that Alt reprogramming the biochip in V's head isn't something that's doable for her. Alt has a lot of power in the digital realm that's for sure, but we don't really know how good her reach into the actual physical world is. Sure she can wreak havoc on 'simple' devices that are connected to a sub-net, like overloading machines and stuff like that. The biochip is a different animal though. It's physically altering V's neural pathways to be favourable to the engram and Alt might not have the ability to alter the physical parts of the biochip that do that, even though she can use the pre-existing physical parts of the chip to transfer an engram's data to V's body.
Even with the blueprints etc Alt may not have access to the equipment in the physical realm that can create a bootleg version of the biochip that is capable of rewriting the neural pathways to be favourable to V. Even if she did, she may need to have a complete map of V's neural pathways prior to being injected with Johnny's engram and getting his/her neural pathways rewired by the biochip. It's likely that nobody has a copy of the neural pathway data for V since she never got hit with soulkiller pre-Johnny, and the biochip is said to be a device that only writes data. The biochip wouldn't have a copy of V's neural pathways stored on it, it would only have what it needed to store an engram on it and rewire the pathways to be compatible with that.
