Do I need to clear out all the Reaper code in Rannoch: Geth Fighter Squadrons?
Solution 1:
You will be at no disadvantage other than your OCD will be screaming at you for not clearing every last bit.
Regardless of how much you clear, the end goal remains unaltered: Reach the data cores and completely rid them of their viruses.
Whether it's "just enough" or "Reaper virus dead to the last", it makes no difference in dialogue or story. Which means I wasted a solid hour in there for no reason.
Solution 2:
Na you should be fine if you don't clear all the code out. It's really getting to the data clusters that is important.