Gary_Drescher comments on A problem with Timeless Decision Theory (TDT) - Less Wrong
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The rules of the transparent-boxes problem (as specified in Good and Real) are: the predictor conducts a simulation that tentatively presumes there will be $1M in the large box, and then puts $1M in the box (for real) iff the simulation showed one-boxing. So the subject you describe gets an empty box and one-boxes, but that doesn't violate the conditions of the problem, which do not require the empty box to be predictive of the subject's choice.
I drew a causal graph of this scenario (with the clarification you just provided), and in order to see the problem with TDT you describe, I would have to follow a causation arrow backwards, like in Evidential Decision Theory, which I don't think is how TDT handles counterfactuals.
The backward link isn't causal. It's a logical/Platonic-dependency link, which is indeed how TDT handles counterfactuals (i.e., how it handles the propagation of "surgical alterations" to the decision node C).
My understanding of the link in question, is that the logical value of the digit of pi causes Omega to take the physical action of putting the money in the box.
See Eliezer's second approach:
Ah, I was working from different assumptions. That at least takes care of the basic clear box variant. I will have to think about the digit of pi variation again with this specification.