I am currently in the middle of a Black Crusade game that takes place prior to the Horus Heresy ever occurring. Their actions essentially influence how the actual Heresy would play out and who would turn to Chaos. My main question is what would have happened if other legions (Loyalist legions specifically) had found out about Sanguinius' gene flaw prior to Horus ever turning? There was talk in Fear to Tread that Sanguinius' legion would have been expunged from Imperial records, but I wanted other thoughts regarding this. Sanguinius was the most loyal out of all factions

Having not read the Horus Heresy books in question I can't give you a definitive answer, however the Legion did not experience the Black Rage before the death of their Primarch at the end of the Heresy. However the Red Thirst was possibly still around during the Heresy and before it. It is likely that the Emperor knew about the flaw, or at the very least suspected it, so the Legion was unlikely to be destroyed like the 2 missing legions. This was the same thing the Emperor decided to do with the Thousand Sons, banning them from Sorcery but not wiping out psychic marines in any of the legions.

The red thirst was around, but in lone, single cases which the legion was able to cover up and hide from...most people.

There was plenty of equivalent stuff in the legions the Emperor either didn't know about or didn't care about - e.g. the Flesh Change (Thousand Sons) or Curse of the Wulfen (Space Wolves). In both those cases, however, we know the Primarchs in charge pointedly didn't let outsiders see what was going on.

Pykers isn't an equivalent thing - psykers can theoretically stop using their powers voluntarily (as Rubio had before he got recruited) whereas geneseed breakdown is something involuntary.

Ultimately, if the Emperor or Malcador decided you either couldn't be trusted, or threatened the glass castle of the 'Unity' myth he and Malcador were trying to ram down people's throats, then events, people or whole groups got quitely airbrushed out of history - see Legions II and XI, the Night of the Wolf, Isafel's memory-tampering with the I legion, etc.

Would Sanguinius ever turn? Probably not. Would someone think he might and do something rash/stupid? Maybe.

If Russ turned up in the skys over Baal instead, it's difficult to figure out what would have happened.

They would not be expunged from records if this flaw were to be found out, the II and XI legions had a separate problem that was far worse then a genetic flaw which caused them to be expunged from imperial records.

Would Sanguinius ever turn? Probably not.

Actually during the heresy this was a distinct possibility forseen by Lorgar. In fact the reason Sanguinius fought horus was that if horus had kept talking Sanguinius knew that Horus would be able to convince him to join the rebellion. Sanguinius threw himself at horus to keep himself loyal.

Actually during the heresy this was a distinct possibility forseen by Lorgar.

Not according to the most recent books. The whole Cygnus malarky was Erebus' idea, not Lorgar's - and in Betrayer , Lorgar tells Erebus to quit wasting his time trying to turn the angels in no uncertain terms:

"I don't care what you think. You will not succeed in illuminating my brother."

Actually during the heresy this was a distinct possibility forseen by Lorgar.

Not according to the most recent books. The whole Cygnus malarky was Erebus' idea, not Lorgar's - and in Betrayer , Lorgar tells Erebus to quit wasting his time trying to turn the angels in no uncertain terms:

"I don't care what you think. You will not succeed in illuminating my brother."

However in Betrayer they also discuss the need to turn Sanguinius to their side or he could possibly stop Horus. Maybe not specifically seen by Lorgar but it was a possibility.