GW has changed both the Warhammer and 40k fluff. Originally (going back to early 90's), the Warhammer world was set in the 40k universe. I think the Realms of Chaos books even had rules for having boltguns and other 40k weapons in Warhammer world. In that setting, Sigmar's arrival was foretold by a twin-tailed comet, and he was found, not born. GW has since revised the 40k fluff to make it clear that the Warhammer world isn't set in the 40k universe. GW also revised the Warhammer fluff to have Sigmar be born and close that debate.
What if the two missing Legions had gone to war against each other over petty differences. If the Ultramarines and/or others had intervened perhaps the primarchs were executed for their actions and the survivors were integrated into their Legions. The remaining primarchs refuse to talk about it due to their shame of how their brothers acted. They were suppose to be above that.
Just my 2 cents
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you have to think, what the hell happened to completely wipe out two legions. there must b a simple explanation. If they went to war with each other and refuted the imperial truth would that b enough?
On all of this, I think they still remain blank because GW is planning something in the future for if the sales go very down...
Lord Macragge and wielder of the Ultramar´s Gauntlets
Possibly one of the two missing Primarchs was Female and the legion of men refused to bow to her and the Emperor refused to allow a female legion to exist...
I may have jsut answered why there are no female SMs!
It were but a joke...
In any case I do not think that we will no for sure the truth behind the 2 missing/lost Primarchs as it is one of the more interesting points of the 40k/space marine background.