The Lost Primarchs of the II and XI Legions

Almost nothing is known about the two lost Primarchs.

References to the second and eleventh Primarchs are made in the short story, The Lighting Tower, in which Rogal Dorn describes the plinths on which their statues stand should be vacant and says that 'no one ever spoke of those two absent brothers. Their separate tragedies had seemed like aberrations. Had they, in fact, been warnings that no one had heeded?'

Also in The First Heretic, Lorgar makes several references saying that the Emperor ordered them to be forgotten. During the time five Word Bearer captains spent being shown secrets of the galaxy by the daemon Ingethel they are shown the Emperor's gene-labs where he is creating the Primarchs and the moment that they were scattered by Chaos. During their time wandering the labs as insubstantial ghosts undetectable as long as they don't touch anything they speak of the two lost legions, mentioning how they were erased from Imperial records and how Roboute Guilliman's Ultramarines legion mysteriously swelled in numbers each time one of the two legions was "erased." The implication seems clear that at least part of the fighting force of the "lost" legions was entrusted to Roboute Guilliman and incorporated into the Ultramarines.

If this is true then perhaps entire chapters descended from the original Ultramarines legion are in fact part of the gene-seed of the two lost legions. At the time of the Heresy remarks made by the five Word Bearers captains Argel Tal, Xaphen, Torgal, Malnor and Dagotal suggest that the fate of the lost legions is relatively common knowledge though kept hushed up. In the intervening ten millennia between the Heresy and the current age of the 41st millennium it is likely this information was forgotten. It is an interesting side-note that the lost legions were numbers two and eleven. Two plus eleven equals thirteen-the number of the Ultramarines legion.
 
The traitor Primarchs in this story are covered with a shroud, so the fate of the second and eleventh is undetermined. They may have been found and befell a tragedy as it implies they were spoken about previously.

In the novel Prospero Burns by Dan Abnett, it is suggested that Leman Russ and his Space Wolves legion had been used by the Emperor in the past to cull/pacify the two legions and that the Emperor had created the Wolves for just an event, utilizing their barbaric, untamed nature as a sort of insurance policy for use against other Space Marine Legions. This is further demonstrated by the unleashing of the Wolves on the Thousand Sons Legion in the same novel.

http://wh40k.lexicanum.com/wiki/Primarchs#Two_unknown_Primarchs