Reading my copy of Inferno, there is an intriguing reference to the two lost legions in the Space Wolves section.
The Rangdan Xenocides appear to be the culmination of the greatest threat the Imperium faced during the Great Crusade. The Rangdan where a threat that almost overwhelmed Imperial forces, whole expeditionary fleets and titan legions where destroyed before the Imperium finaly got the upper hand.
Allow me to quote from Inferno:
"Whole Expeditionary fleets went
to their deaths without a single survivor,
worlds were laid waste, dozens of Titan
Legions were obliterated and by the end,
entire Space Marine Legions [REDACTED
SECTION] lost to the Imperium. Much of
what happened during this abyssal conflict is
still locked under seal, but what can be said
is that with the breaking of the Labyrinth
of Night by the Emperor, the threat was at
The assumption that the two lost legions had done something so bad that they had been wiped from the records, somewhat backed up by Fear to Tread, may not be the whole truth. Perhaps it was the EVENT that led to the legions being lost that caused their removal from imperial records rather than the actions of the legions?
Inferno states that the 1st and 6th legions had the clean up job after the xenocides which led to some of the dark reputation for these legions and the mutual respect between the Dark Angel's and Wolves. The Rangdan's nature implies that the 1st and 6th legion had to cleanse planets, killing civilian populations.
So the lost legions could of been affected in some way that meant their destruction was required or it could be due to some great battle or secret that led to their destruction that had to be removed from the records.