Yes, but… —
From the 40K Fandom wiki:
The Emperor and Alpharius
Alpharius Omegon during the Great Crusade. Following his discovery, however it occurred, eventually Alpharius was taken back to the epicenter of the ever-expanding Imperium and reunited with his father, the Emperor. There was the usual rejoicing, pomp and circumstance, but records on Terra suggest that the two spent little time together. Alpharius was quickly sent to take command of his Legion, while the Emperor had many pressing affairs of state by this time late in the Great Crusade era.
Alpharius and his twin-primarch brother Omegon shared the same physical appearance and together served as joint-primarch of the Alpha Legion. The Emperor was aware of Alpharius Omegon's secret; but whether the creation of the twin primarchs was intentional or not remains a mystery.
—… When?
The details of Alpharius Omegon’s recovery are mysterious and unsettled. The wiki summarizes this:
Of the many mysteries that surround the Alpha Legion, the most fundamental and key enigma is the question of the Alpha Legion's primarch, Alpharius. Of all of the primarchs who remained to draw blood against each other in the Horus Heresy, of Alpharius the least is known for certain.
Furthering this mystery and the outright deception perpetrated by Alpharius, many reliable accounts of his origins differ.
It then proceeds to list no less than four wildly differing accounts.
What we can be certain of is whether it was Horus “shaking the hornet’s nest” or the Emperor himself who discovered him, it was roughly in the same ballpark amount of time for Alpharius Omegon to have established his own mini-Empire; he was the final (twin) Primarch reclaimed.
Omegon’s existence was a closely held secret; from the wiki again:
The existence of the twin primarchs of the Alpha Legion was known only to the members of the Legion itself, and was a well-kept secret even from the other Astartes Legions.
We know that as of Deliverance Lost the Emperor is aware of both Alpharius & Omegon, because this is addressed as part of the storyline in the book. However, we are not given details about how or when the Emperor came to know this information.
