This letter puzzled me for several weeks. The poem My Silence Knot has always seemed to me to contain an unsolvable mystery, but I think I've finally found something reasonably simple that fits without causing too much trouble to established facts. I think the solution that Beatrice loved Lemony very much and wanted to marry him, and he just didn't get a message, fits the theme of TBL and Lemony's life. It's true that as you pointed out, this way of thinking leaves some loose ends, but it's the same loose ends left by LSTUA when it comes to Lemony's canceled wedding. The coded message Sebald sent to Lemony by the wedding venue organizers indicated that even before Lemony's escape, there were rumors that he had died. Also, for some reason only Lemony was told to flee abroad. Jacques did not think it necessary for Bestrice to flee, despite the message that Olaf would kill Beatrice as well. I think Olaf's hatred was for Lemony, and Beatrice would be killed just because she was related to Lemony. According to the message, Olaf posed a physical threat to the two, but Lemony's escape abroad would apparently protect Beatrice as well, as long as Lemony didn't try to contact anyone. Probably Jacques' plan was to bolster the rumors about Lemony's death. But when Lemony contacted Beatrice, whatever kind of danger he posed to her, it had to be a real danger to the point where she obeyed his instructions to send the letter.
Glad to hear you're halfway through my book! I hope you're having fun.