Let us assume, for the sake of discussion, that before Passover I appointed an agent to carry out the sale of my leavened food to a gentile, but it is uncertain whether the agent actually carried out his mission, and this cannot be clarified. Because of that doubt, I also performed nullification of the leavened food in case the agent did not carry out his mission. Now, after Passover, if I make use of the leavened food, the nullification will be retroactively uprooted, and it will then turn out that retroactively there was a Torah prohibition here of “it shall not be seen and it shall not be found.” According to this, seemingly this is a Torah-level doubt, no?

The question is not whether one transgresses “it shall not be seen,” but whether one may eat leavened food that remained over Passover. Retroactively turning the leavened food into non-nullified leaven does not mean a retroactive violation of “it shall not be seen.” True, in the Talmudic passage in Nedarim 14b it seemingly proves the opposite—that it is forbidden to eat today lest tomorrow it become clear that this was a prohibition—but one can distinguish in several ways. There, he performs the act of eating today while knowing there is a concern that tomorrow he may sleep. Here, at the time of the nullification, he is not entertaining the thought that he is about to undo it. Beyond that, I once argued that in that passage this is not the conclusion at all. Something similar is discussed by the Ritva (and Rabbi Kook has a responsum about this) regarding someone who recited a blessing over food and then changed his mind and no longer wants to eat: is he obligated to eat in order to “save” the blessing? He writes that there is no obligation to eat, though the reasoning is open to discussion: is it because such a blessing is not considered in vain, since at the time it was needed, or because there is no obligation to “save” blessings? I also once discussed, in light of all this, a woman who was divorced conditionally and then married someone else. Is she forbidden to violate her condition after the marriage, since by doing so she would turn her acts of intercourse retroactively into forbidden ones (and her children into mamzerim)?
There is a great deal to say about this, but in my opinion there is only a rabbinic problem from this point onward, not a retroactive Torah prohibition.

One should also add a question about the basic premise itself. During Passover itself, the leavened food was indeed like dust in his eyes (for it is considered dust only because of the prohibition, since we are dealing with leavened food that is intrinsically fit for use and he rejects it only because of the prohibition), and now he wants to restore it to use; therefore the nullification is not necessarily void retroactively. Only if he were to eat the leavened food during Passover itself would that clarify retroactively that the nullification was not serious.

By the way, there is a presumption that an agent carries out his mission.

Seemingly the discussion here is about a Torah-level doubt that rolled over into a rabbinic one, on the view that the nullification is ineffective, and the later authorities discussed this at length. But it is not clear why the nullification should be undone because of use after Passover; after all, the nullification during Passover was wholehearted. It is like declaring an object ownerless and then later reacquiring it (see Bava Kamma 28a).

That comparison depends on the dispute among the medieval authorities about what nullification actually is. You are assuming that it means declaring it ownerless. But if nullification means rendering it like the dust of the earth, then logic suggests that a change of mind alters the status retroactively. However, in light of what I wrote above (that the issue is the prohibition and not the object itself), that is true only for a change of mind during Passover itself.

If at the moment of nullification before Passover I knew that after Passover I would use the leavened food, does that mean that the nullification was not wholehearted? In other words, in this case it’s not that I later changed my mind about using the leavened food; rather, from the outset I nullified it in case the sale did not take effect, while knowing that I would use the leavened food after Passover on the possibility that the sale did take effect.

That does seem likely. Even so, there is still no contradiction to my claim that if this was not known in advance and you later changed your mind, the nullification is not void retroactively.

I have now seen some sources here regarding doubt about leavened food that remained over Passover:
http://din.org.il/2018/04/24/%D7%A1%D7%A4%D7%A7-%D7%97%D7%9E%D7%A5-%D7%A9%D7%A2%D7%91%D7%A8-%D7%A2%D7%9C%D7%99%D7%95-%D7%94%D7%A4%D7%A1%D7%97-3/