Particular counterfactual instances of you can't influence whether they are counterfactual or exist in some stronger sense.
What can influence things like that? Whatever property of a situation can mark it as counterfactual (more precisely, given by a contradictory specification, or not following from a preceding construction, assumed-real past state for example), that property could as well be a decision made by an agent present in that situation. There is nothing special about agents or their decisions.
What can influence things like that?
Why do you think something can influence it? Whether you choose to cooperate or defect, you can always ask both "what would happen if I cooperated?" and "what would happen if I defected?". In as far as being counterfactual makes sense the alternative to being the answer to "what would happen if I cooperated?" is being the answer to "what would happen if I defected?", even if you know that the real you defects.
Compare Omega telling you that your answer will be the the same as the Nth digit of Pi. That doesn't you allow to choose the Nth digit of Pi.
According to Ingredients of Timeless Decision Theory, when you set up a factored causal graph for TDT, "You treat your choice as determining the result of the logical computation, and hence all instantiations of that computation, and all instantiations of other computations dependent on that logical computation", where "the logical computation" refers to the TDT-prescribed argmax computation (call it C) that takes all your observations of the world (from which you can construct the factored causal graph) as input, and outputs an action in the present situation.
I asked Eliezer to clarify what it means for another logical computation D to be either the same as C, or "dependent on" C, for purposes of the TDT algorithm. Eliezer answered:
I replied as follows (which Eliezer suggested I post here).
If that's what TDT means by the logical dependency between Platonic computations, then TDT may have a serious flaw.
Consider the following version of the transparent-boxes scenario. The predictor has an infallible simulator D that predicts whether I one-box here [EDIT: if I see $1M]. The predictor also has a module E that computes whether the ith digit of pi is zero, for some ridiculously large value of i that the predictor randomly selects. I'll be told the value of i, but the best I can do is assign an a priori probability of .1 that the specified digit is zero.