We also wouldn't know if various ecuмenical councils were actually approved by a real pope and not by some imposter, or someone who was installed after a Siri-style resignation under duress(a cardinal Siri-esque figure in the 500s or something would be completely lost to history). There's effectively nothing we could be sure of.
I suppose you could apply the question of positive and negative doubt - we know of reason to doubt the 1958 Conclave but not the 1939 Conclave(as far as I know). Still, reasons to doubt past conclaves could've simply been lost to history, so it doesn't seem like a tenable position to me.
This is basically my objection to the Siri scenario. If you say that all the cardinals can come out of the conclave and say they elected a pope, and all of them be lying, this basically destroys any way to know for certain who the pope is. It is a historical fact that not one single cardinal from the 1958 conclave ever denied that Roncalli was elected. The closest you can get is that Siri himself was asked if he was elected and he gave an evasive answer. And this is only in a private conversation that was not on what you could call the public record. In other words, not that I really think those Frenchmen are making the conversation up, but honestly we only have their word for what they claim Siri said. It seems hard to reject an entire papacy based on something like that.
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In the bigger picture, this could call into question almost any conclave if this were possible. Someone could come out years later and claim that the reigning pope bribed the Cardinal of Mogadishu, for example, with a trainload of rocket-powered grenades so he would vote for him. Or some janitor for the conclave could come out later and say he found a note in one of the cardinals' wastebaskets that he wrote to another cardinal promising him something if he voted for him. Or the waiter who serves their midday meal could say he saw one of the cardinals staggering a little on his way out of the refectory because he drank a little too much limoncello afterwards, so his vote is in doubt because he was drunk. The possibilities are endless, and believe me, there is no shortage of people who are ready to come forward with stories like this, true or false. Stuff like this is exactly how the Great Western Schism started. I grant that doubts about Roncalli's papacy involve far more serious questions than bribery or conclave gossip, but I think it's inherently a weak argument to say he wasn't pope because something went wrong in the conclave. The Church deliberately makes it as hard as possible for people to know what goes on in a conclave, for precisely that reason, so that no one could use conclave shenanigans to question a pope's claim to the papacy.
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While I grant that most of what Roncalli did during his reign(?) raises solid reasons to question his orthodoxy, I have a hard time seeing that the stories the Siri thesis involves really indicate that much. I say let's stick with what we know for certain, starting with Roncalli's public record as pope(?).