Could this be the dénouement?
Hmmm. I think I may have stumbled upon a plausible resolution for several crises and mysteries. Tell me what you think of this scenario ...
After five years of stasis -- thirty months from now in story time -- Mechanicsburg un-freezes. Agatha and Violetta have been waiting for this, and as soon as the stasis field is gone, they race to the Cathedral to rescue Tarvek.
And they're too late. Tarvek is DEAD, and he's already decomposed far beyond any hope of revivification.
Some time later, Agatha gains access to the Time Window apparatus. (This may be when Bang saw her using it, or it might be on some other occasion.) Agatha has a plan -- perhaps suggested by Othar! -- that might allow her to save Tarvek after all. She can't rescue his body without creating a huge temporal paradox, but she can rescue his mind.
Seconds after Tarvek is hit by the poisoned dagger, Agatha zooms in and attempts to transfer his mind to a new body. But wait! There's a complication! The stasis field has altered the energy level of the Cathedral environment. She can't transfer his mind into another body in her own era.
But she can transfer it into a mind two centuries earlier. So Tarvek is downloaded into van Rijn's brain, allowing him to live a full life and to set up the various McGuffins (Otilia, Moxana's prophesies, van Rijn's notes, and so on) ... Perhaps Tarvek even meets a much younger Higgs and briefs him on what's going to happen. (UPDATE: Tarvek might even tell Higgs to be on a particular Wulfenbach airship so he'll be in a position to save Klaus' life.)
And one more wrinkle: Tarvek gets to marry Agatha after all! While observing Euphrosynia, it becomes clear to Agatha and others that she is Pure Evil. She's also doing things that are contrary to the legend, and unless she's stopped she will irreparably alter the timeline. So Agatha downloads a copy of herself into Euphrosynia's brain. Agatha-in-Euphrosynia goes into hiding right under Andronicus' nose -- with van Rijn! Eventually Andronicus wanders off to search the world for Euphrosynia, and Tarvek and Agatha live happily ever after.
And "meanwhile" two centuries later, Agatha and Gil finally get together.
UPDATE: There are two things I don't like about this scenario:
☹ What happens to van Rijn's original personality? Do he and Tarvek cohabit? Merge? Time-share? Or does Tarvek overwrite van Rijn? Does van Rijn accept Tarvek's mind willingly, or is he so evil that obliterating his personality is actually a good thing?
☹ If Tarvek is DEAD-dead and is too decomposed to be revived, then what was the point of the the long Si Vales Valeo sequence in Castle Heterodyne? The justification for that in storytelling terms was that Tarvek had died and been revivified, thus making him ineligible for the Lightning Throne in the eyes of the Fifty Families ... and since only Gil, Agatha, and a few others know that this happened, they can use their knowledge as leverage. If Tarvek dies from Tweedle's dagger wound, that entire segment of the story arc lacks any reason to exist.