What do you think the "years later" references mean?

[Dante]

Strictly speaking, it's Klaus who would lie awake for years regretting not sending Stephano back with the taxi driver (TRR p. 44). Well, in the later books it's reasonably clear that the author was reassessing his ideas of how long after the Baudelaires' experiences their history was being written by Snicket, and additionally he was doubtless preparing for a more open and ambiguous ending, which makes two good reasons not to discuss the Baudelaires' future. It's unlikely that this would have been planned out in TRR, though, and quite likely the line was inserted without thinking about it. As to how to explain this canonically - perhaps Klaus wrote about his regrets in the island volume A Series of Unfortunate Events, which takes us up to a year and likely several months since TRR, which might be good enough.

[Dante]

It's the same book, so same difference - but I think it would be worth emphasising Snicket's statement that he "cannot say" how Violet slept specifically years later, and can only give a general picture of her feelings. Certainly I don't think we can take "always" very seriously.

[Dante]

Unless you're suggesting that Lemony Snicket is either literally omniscient or had a chat with Violet on her deathbed and outlived her, he cannot possibly know what she always felt.

[Foxy]

I wonder if Snicket rewrote the earlier books he wrote under his original contract to fit better into the entire V.F.D. plot, how different the first four books would be. He would leave out probably the details about the kids years later in TRR, and somehow find a way to pull Monty and Josephine more clearly into V.F.D. Although, he knew about V.F.D. when he wrote TVV, but Hector was not seemingly in V.F.D., although we find out later in ?1 he was in V.F.D.

I guess the point I'm making is there are some "errors" in the first few books, some slip-ups, I guess. Nobody can write a perfect story.

[Optimism is my Phil-osophy]

You know my deep opinion on the subject, and I don't mind repeating it over and over and over and over ...

I agree that Daniel Handler would like to change the story after he had some ideas. But he did not. Instead, he created confusion, seeking to give the open-ended impression of their survival, but ultimately there is evidence that Daniel Handler remained with the idea that the Baudelaires survived. The only thing he did was shuffle the timeline in our minds, through purposeful repetitions of events, and lies and / or deceptions from an unreliable narrator. I'm not saying that he planned it all from the start. I am saying that he was adapting the story narrated by Lemony, so that the story is confusing and at the same time does not contradict itself.
Take for example Lemony's apparent omniscience, accidentally quoted by Dante. Lemony's apparent omniscience about people's thoughts and feelings exists only with the Baudelaire siblings. He does not claim to know about the feelings and thoughts of characters other than themselves. Lemony knows about Baudelaire siblings 'secret dialogues, but doesn't claim to know about other characters' secret dialogues. The justification for this is that Lemony read about what the Baudelaire siblings wrote in the island book. Daniel Handler arranged this explanation (explicitly) only in book 13. This necessarily puts Lemony writing about the past. If you consider LSTUA does not present fraudulent documents, you will also notice that Lemony's letter to cheesemakers talking about the movie Zombies In the Snow reveals that he tried to publish the books through other means, before publishing through the current publisher. Cheesemakers was the penultimate chance to make Baudelaire siblings-related events known to the general public. And of course ... Prufrock Prep has been closed for many years when Lemony wrote TAA. Lemony in TSS stated that she was researching for several months the events related to the events involving the Baudelaire siblgins in the mountains. So Daniel Handler never abandoned the idea that Lemony was writing about the past.
The secret letter in TSS is just a Red Haring to confuse our mental timeline of Lemony Snicket-related events.

[453]

I must say I'm glad Lemony opted, in the end, to publish these events as books rather than engraving them into wheels of cheese, which are liable to be eaten or covered with mould.