- It hasn't really been retconned, we just learned new information regarding the events.
- Magnus did retreat to the Eye of Terror with the bulk of his legion...
- And they reentered real space once the survivors were "safe."
- Not all his legion was on Prospero for the attack either.
The events of Warhammer 40,000 are not chronological by any means. GW gives us bits here and there about what happened and then they fill in some of the blanks (some that we didn't even realize were there) at a later date/time.
Personally I have always seen the events of 40k on a massive timeline and GW keeps releasing new information we didn't have before on that timeline in random places as they determine we are ready to learn them. The events of the Thousand Sons during the HH are one of these...
So, Magnus retreated and took the survivors of Prospero to the Eye of Terror, but nothing ever explicitly said that he stayed there or, more directly, that he did not participate in the Horus Heresy. It also never mentions anything about Magnus following the battle or even that he lost his physical form. This new information we learned much later about the battle.
As we now know, following the battle, the Thousand Sons retreated to the "relative" safety of the Eye of Terror. After battling Leman Russ, Magnus was in a near death state and ended up being "broken into shards" that his followers where working to collect. As Ahriman and Co. searched for the shards to restore their primarch they didn't really "participate" in the HH, as their primary goal was to help Magnus.
As Magnus was being "rebuilt" he learned that one of his shards was on Terra. Wanting to be as he was before his agreed to accompany Horus with his assault on Terra, but this was mostly to get himself there to recover his shard than aid in the plan to destroy the Imperium.
Note that in addition, each legion was not all travelling the void as one massive force. Some units were here, some were there, and etc. all spread across the galaxy. This was also the case for the Thousand Sons. Though they were never really a large legion they still had much of their number engaged on distant battlefields during the attack on Prospero.
After learning of the battle these units likely had no direction given the legion being in chaos (and Chaos coincidentally) and we don't know how much communication the legion actually maintained with their scattered forces. Some of their number joined other battles, though we don't know if this was under direction or because they believed they were the last of their legion.
While we learn information regarding the events of the 40k universe we have to remember that the universe is vast, we can't know everything that happened, and much of what was known of those times has been lost...