Someone who was told that a Torah-level doubt must be treated stringently as certain—is he considered inadvertent? Of course the law is that he is intentional. The Shev Shema’tata 1:3 writes that according to Maimonides he would be liable to bring a sin-offering, even though by Torah law it was permitted for him; nevertheless, since the Sages prohibited it, he cannot be considered under duress. But according to Rashba he certainly gets lashes, as Tosafot wrote in Yevamot 80a.

Of course (!) and certainly (!) the law is that he is intentional and gets lashes? I liked the decisiveness. And in Shev Shema’tata there he wrote that he is intentional and therefore liable for a sin-offering? Are you sure you wrote that while awake? 🙂
As for our issue: first of all, this certainly is not connected to the question whether it is treated as certain or not. The question is whether, when one violated the prohibition involving a doubt and it was discovered that he ate forbidden fat, he is liable as though he had eaten intentionally. As I wrote, he is not intentional with respect to the prohibition itself. This is an uncertain warning, and you cannot give him lashes for that. I find it hard to believe that anyone would disagree.
Tosafot in Yevamot there is proof to the contrary. They assume that he does not get lashes in such a situation, since this is an uncertain warning. Therefore they write that the doubt of whether someone is an adult or a minor is different, because when it is clarified retroactively that he was an adult, it turns out that he received an ordinary definite warning, and therefore gets lashes. But that is not true לגבי someone who was warned regarding a doubtful prohibition (whether forbidden fat or permitted fat), and that is obvious.
As for liability for a sin-offering in such a case, that is a different discussion. Of course liability for a sin-offering applies to inadvertence, not intentional sin. And indeed in such a case, as I wrote, he is considered inadvertent and is liable for a sin-offering. This is probably also true according to Rashba, as he himself writes in Shevuot 18, regarding someone who violated rabbinic menstrual-cycle regulations and the woman was found to be a menstruant, that he is liable for a sin-offering as an inadvertent sinner (and is not considered under duress because he had been warned by the rabbinic prohibition). Presumably the same would apply to someone who was warned because of the prohibition stemming from doubt, whether according to Rashba or according to Maimonides: he would be considered inadvertent, not under duress, regarding the eating of forbidden fat, and would be liable for a sin-offering. That is what I wrote.

Because of the sharpness, the Rabbi missed a word.
If a Torah-level doubt is treated *as certain*—I was using the questioner’s terminology.
The point is that according to those who hold that a Torah-level doubt must be treated stringently by Torah law, if it turns out that the matter was forbidden, he is liable for lashes because he is intentional, since by Torah law he was forbidden to eat it. Of course there is a problem with the warning, and it will depend on the dispute whether an uncertain warning counts as a warning. The issue is what type of liability he has—lashes or a sin-offering; intentional or inadvertent.
But according to Maimonides, by Torah law it was permitted for him to eat, and therefore it is obvious that you cannot make him liable for lashes.
(By the way, Rabbi Shimon Shkop in Gate 1 wanted to prove from the sugya of whether an uncertain warning counts as a warning that even according to Maimonides one gets lashes if it turns out that the thing was forbidden, and from this he sought to prove that even though one is permitted to eat it, in any case one gets lashes because lashes apply to the object of prohibition itself. But in truth we do not find anywhere an uncertain warning in a case that, according to Maimonides, one was initially permitted to eat; all the cases are of one piece out of two pieces, where the medieval authorities wrote that Maimonides agrees that it is forbidden.)

1. I didn’t miss that word. I addressed it explicitly.
2. Whether a Torah-level doubt must be treated stringently by Torah law or by rabbinic law is a different question from whether it is certain or doubtful (here the question is whether there is a prohibition on entering the state of doubt itself, or whether it is only a concern of prohibition that one must be stringent about, and only if it later turns out that he violated an actual prohibition is there really a prohibition here).
3. Even according to Maimonides, who holds that a Torah-level doubt must be treated stringently only by rabbinic law, he can still be held liable if it later becomes known to him. That is the law of menstrual cycles that I mentioned from Shevuot 18 and Rashba there. And not necessarily because one gets lashes for the prohibition itself, but because the rabbinic prohibition serves as a warning and removes the claim of duress. An example is that according to Maimonides one is liable for a provisional guilt-offering for an established doubt of prohibition even though by Torah law it is permitted (and what they wrote in his view to distinguish between an established and unestablished prohibition, as you yourself noted, as well as the distinction between capital prohibitions and others, is contradicted by his own wording. In my article on the guilt-offering I showed this, and also explained why the law of the provisional guilt-offering is not difficult for him. It reflects a misunderstanding of the nature of guilt-offerings).
4. As for later discovering it, that is an interesting question. In the case of a provisional guilt-offering, if he later discovers it, he brings a fixed sin-offering. This is explicit in Maimonides, Laws of Errors 8:1. See also Sefer HaChinukh commandment 128. However, one can infer from his wording that this is only if he erred in the doubt, not if he intentionally violated the prohibition of doubt. But it is unclear whether he means that there was inadvertence regarding the very law of the provisional guilt-offering—meaning that if he was not inadvertent, he does not bring it—or whether this also applies to the case where it later became known, in which case he would not bring a sin-offering. In any event, Maimonides does not write that he gets lashes, and I am not familiar with such a claim in his view.
5. According to the view that an uncertain warning is not a warning, of course he does not get lashes. However, according to the view that it is considered a warning, there is room to discuss it, because it seems that at least an uncertain warning was present here. But even that is only where there is definitely a prohibition here—an established prohibition. Where there is no established prohibition, it is very implausible to view this as an intentional prohibition that incurs lashes. And there is clear proof of this from Shevuot 18a regarding menstrual cycles.
6. The Tosafot you cited is proof that there are no lashes here.
7. For some reason, the accepted halakhic ruling that an uncertain warning counts as a warning is plainly not about all cases of doubt. It applies only to a prohibition linked to a positive commandment, where there is definitely a prohibition and only a doubt as to whether he will rectify it; there Rabbi Yohanan and Reish Lakish disagreed. This was also noted by the commentators on Maimonides, Laws of Sanhedrin 16:4. See there in Radbaz and Kesef Mishneh, and especially Even HaEzel. This also explains why the medieval and later authorities assume as obvious that one does not get lashes for an uncertain warning (and they always raise the difficulty regarding this or that case that it is an uncertain warning. But after all, the halakhic ruling is that an uncertain warning is a warning).
8. For some reason, you keep writing as before that one brings a sin-offering for intentional sin.

I’ll start from the end.
I didn’t see where in my words I wrote that one is liable for a sin-offering for intentional sin.
The discussion at the beginning was whether someone who transgresses a Torah-level doubt that must be treated stringently is considered intentional or inadvertent.
Of course, assuming he is intentional, he needs a warning in order actually to receive lashes, but he certainly does not bring a sin-offering.
Simple reasoning suggests that according to Maimonides there is no way to give him lashes, because even if the Sages prohibit it, you cannot say about a person that he committed an offense when the Torah permitted him to do the act. True, the Sages prohibited it, and he is not under duress, but the exemption is not because of duress; rather because the Torah told him that he is permitted to do this act.
And in order to invent lashes, Rabbi Shimon Shkop came up with the idea that the lashes are not for the offense of disobedience, but for the object of prohibition.
But without that innovation it is obvious that according to Maimonides the law is that one does not get lashes. What can still be discussed is whether he is inadvertent and brings a sin-offering, or whether after the Sages prohibited it he is no longer considered inadvertent—and Shev Shema’tata wrote that he is liable for a sin-offering.
The question is according to Rashba.
And certainly, as long as it has not been clarified that the thing is forbidden, one cannot give lashes based on doubt. It is only regarding a doubtful sota, which is treated as certain, that Tosafot in Yevamot 11 and Tosafot in Sota 28 disagreed whether she gets lashes before it has been clarified.
The question is what happens when it is clarified that the thing was forbidden.
And since it was definitely forbidden to him from the outset, it does not seem possible to say that he is inadvertent and should bring a sin-offering.
The question is whether there are lashes, and on this it seems clear from Tosafot in Yevamot that when it becomes definitely clear that there was a prohibition, one gets lashes (as Shev Shema’tata inferred there, and there he wrote that according to Maimonides there would be a sin-offering because he is considered inadvertent, and he is not under duress because the Sages prohibited it).

If the original act was a permitted act, then you also cannot bring a sin-offering for it. The reasoning that one can bring a sin-offering comes from the Talmud in Shevuot. You get lashes for the fact that you transgressed, and you do not have an exemption claim of duress because the Sages warned you.
Tosafot in Yevamot says the opposite.
All right, we’re repeating ourselves.