I have listed a few possible ancient astartes conspiracies and how they might affect the recent M41 -situation. The cool thing about these are that they go, so to say, "Beyond the Canon", so while there is material that hints to the possibility there is actually nothing that would outright say how the things really are... as always, I am interested in any comments, suggestions and feedback you might have
Imperium Secundus
Canon facts: During Horus Heresy while writing Codex Astartes Guilliman had a contingency plan called "Imperium Secundus". The real contents are not known. After Horus Heresy Guilliman became the Lord Commander of Imperium, Codex Astartes became the standard guidebook for almost all Astartes and more than 50% of all chapters come from Ultramarine geneseed.
Ancient conspiracy: What if it was Guillimans intent right from the start to let the other legions bear the brunt of fighting against Horus, save his own legion and establish his own lineage as the ruling elite of the "Second Imperium"? So Codex Astartes was not written to make Space Marines more effective, but actually to castrate the fighting power of other legions by fragmenting them and to reinforce the status of Guilliman himself by forcing everyone to play by his "playbook"... Then, while acting as Lord Commander, Guilliman made certain procedural adjustments to the way new chapters are created to ensure that his geneseed would be used in future. Guillimans full plan was probably never realized in full as he was poisoned and put into stasis, but his genetic and spiritual legacy forms the basis of vast majority of all Astartes still.
How to use: If this was even remotely true it would probably be one of the most horrible secrets in the whole Astartes community and any Ultramarine (not to mention any other Codex chapters who would know of it) would be ready to do ANYTHING to keep it a secret. Hell, since exposing this kind of ancient treachery would risk renewing old conflicts between Ultramarines and descendants of other legions and thus pose a huge risk to the Imperium itself even High Lords of Terra would be inclined to keep the secret firmly buried. Of course there is also the possibility of some sort of "Shadow Council" of Ultramarine descendants that still try to work out the old plan and control the destiny of Astartes and Imperium behind the scenes...
The Darkest Angels
Canon facts: Dark Angels have their secrets. A lot of them. All related somehow to their old Horus Heresy civil war. Dark Angels believe the Fallen are scions of Chaos and all corrupted. Accordingly the interrogated Fallen claim that Fallen are the "true heirs of the legion" and Forsaken are the traitors who purposefully left the Emperor alone not taking part in Terra conflict.
Ancient conspiracy: What if Lion was hedging his bets and purposefully kept his Legion back from the Terra with the idea of first seeing who wins (Horus or Emperor) and then joining the winning side? What if after Horus dies and Emperor is disabled and incommunicado Lion is still "playing it safe" and purposefully left his Legion divided so as to make sure his genetic legacy will be preserved no matter who comes out in top?
How to use: If this was true then it would probably be something very, very few know about. Maybe Lion and whoever was working with him actually spread two conflciting "truths" to the two parts of his legion. Maybe no-one knows about the original plan anymore and both Fallen and Forsaken work exactly according to what their primarch wanted, without even realizing it anymore. Or maybe there is a small "inner circle within inner circle" that keeps the conflict between Fallen and Forsaken going but limit it so that Forsaken can never kill off all Fallen...
Space Shark Mystery
Canon facts: Space Sharks/Carharodons operate outside Imperium and all Imperial control. There is no sure knowledge on when or why they were created and whose geneseed they come from (Raven guard is strongly suspected). Earliest notes of them come from 888.M32 which means they must be either 2nd or 3rd founding chapter. Raven Guard has a "dark secret" of having used cloned marines during aftermath of Istvaan catastrophy.
Ancient conspiracy: What if Carharodons are not of any official founding at all? Maybe they are, so to say, the "Black Templars of Raven Guard Legion" meaning they are the part of the Raven Guard that did not accept Codex Astartes? To keep up the appearances Corax removed these guys from the Legion before adopting Codex Astartes and gave them enough equipment from his former cloning facilities to secure that they could store and implant their own geneseed. Maybe even their original equipment is gathered from what was left from the cloned Raven Guard abominations when Corax put the abominations to the sword.
How to use: If this was true it would make the Carcharodons a true "self-made chapter" originally of no founding at all and answerable to no-one else. And they would probably know it but try to keep it secret. Also, if it was possible for "self-made chapter" once, is there any others of such out there?