I was just skimming the material and looking to see if he ever had a plot where someone goes after Frodo and Sam. No luck so far. I should add an in depth reading of "History of LOTR" just to make sure. :)
I was surprised that an early plot had Merry and Pippin wandering away and no one going after them (poor hobbitses!) Or was that the plot line where Aragorn thought all four hobbits were together? It gets confusing after a while!
In the movie it's clear when Frodo and Aragorn talk that Frodo must go on alone. Aragorn recognizes that.
But in the book, when they're first discovered gone it's not until they discover the missing boat that they realize what has happened.
But I think you already knew that...;-)