It should be "two" in your example ("He replies that the two act on different time scales."). Using "twos" is wrong.
If it's helpful, you can think of it as having omitted a noun, like saying "the two" instead of "the two processes".
It's in general quite uncommon to pluralize numbers. Some examples I can think of are the expression "in twos" like, to say something comes "in twos" (= in pairs), and when you're actually using "two" as the substitute for a noun, like "the number two" ("No twos were drawn."), or the playing card ("I have three twos in my hand."). For a more complex example, one could say "I have two twos in my hand", or, closer to your use case, "I have the two red twos in my hand."