A friend of mine brought up the possibbility that, since Jacques is mentioned as looking for Lemony in TCC, and that comment is a throwaway line from Lemony as the Baudaelaire biographer, could we presume that the Snicket brothers met up prior to Jacques's death? If so, Lemony bringing up that Jacques wanted to know whether or not he's alive could have been meant as a signal for Kit, which would than explain the inclusion of the letter one book later (Kit obviously never read ASOUE, but could either have received communication from Jacques that she dismissed, tired of hoping Lemony was alive, or never got any message, which is why she believes both her brothers are dead by TPP).
Could you remind us of what exactly this line in TCC was? I only remember a line about the two of them having stayed in the guest caravan at the carnival once a very long time before. At any rate, the history of when people believed Lemony to be dead and who knew the truth has always been extremely vague; I recall it being something of a surprise to us in The End when we learnt that Kit believed both her brothers to be dead.
The line is: "If Jacques Snicket or another volunteer steps inside and asks me if his brother is alive, I tell them.", chapter seven, page 157. Interesting that a lot of you were surprised about Kit thinking both her brothers were dead; I remember just feeling sad, because it meant she finally gave up hope some time after her letter in TUA where she talks about grabbing newspapers that blow by. I think that's why I'd like this reunion idea to be plausible; no matter how you personally view Lemony's many death stories, when they were spread, and how long people knew about them, I think you could say both Kit and Jacques probably denied them the longest, and it'd be nice for one of them to be proven right before dying. And yes, I know it goes against all of Snicket's warnings to want someone to be happy and have their hopes realized, but it's temporary.