Isstvan 3 is the site where the Sons of Horus, Death guard, Emperor's Children and World Eaters killed most of the loyalists in their legions.
The Thousand Sons are a special case since they didn't plan to be traitors. This leaves 4 traitor legions who's loyalists were not killed there:
Are there any official stories about any of these legions culling loyalists around the same time?
Word bearers
In The First Heretic, Erebus remarks that they had to '
cleanse' some less than zealous brothers.
And when Argen Tal pressed on the number, it was made out as quite a few. This shows the Word Bearers did purge their ranks in a similar fashion to the other Traitor Legions, they just did it earlier and in a less drastically obvious fashion.
We are also told that all Terran-born Word Bearers were killed over the course of the half-century or so between Monarchia and Istvaan V, chiefly by an organisation called the Brotherhood. It comes up in Anthony Reynolds' post-Heresy Word Bearer trilogy as well as in Betrayer, where Argel Tal speaks of it as a
"trickle down the decades" - the potential Imperial loyalists just die off, slowly, carefully and in ways that no doubt appear totally innocent.
Notably, the Word Bearers are also the only Legion to undergo a second purge, where Lorgar sends the most fanatical haters of the Ultramarines to martyr themselves at Calth.
Night Lords
in Prince of Crows Curze, on being asked why he didn't purge his legion states "I wouldn't know where to begin and where to end" he saw his whole legion as corrupt so was not going to start killing off parts of it when he saw the whole lot as diseased.
so there was no official purge a la Isstvan III or the internal purging that the Word Bearers did. However, Horus Heresy Book Two: Massacre raises the possibility that there was some conflict between loyal-ish and traitor Night Lords elements during the events of the Dropsite Massacre. In addition, we know from Horus Heresy Book Six: Retribution that there were significant Night Lords Legion elements (company or larger) that remained loyal to the Emperor en mass and were not otherwise purged/hunted down by their brothers.
Iron Warriors
In the Age of Darkness anthology Barabas Dantioch is offered a choice by Warsmith Krendl to join the heresy, he refuses and so Krendl attacks him.
I imagine given how strung out and separated the Iron Warriors where a concerted Purge was difficult to achieve so post Istvaan individual groups where approached and either joined, where killed, or joined the Loyalists as Dantioch did. In addition I am sure I read somewhere that members of the Iron Warriors attempted to stop the bombing of Olympia and where gunned down by there fellow Iron Warriors. There are suggestions that Iron Warrior Loyalists made up the bulk of the company that would eventually become the Scythes of the Emperor.
Alpha Legion
Nothing is known, there are hints that either the whole legion is actually Loyalist and working to stop the Heresy the only way they know, from the inside, that the legion is split with Alpahrius and Omegon each having a different aim, or it is possible there was a Purge, but if there was I imagine no Alpha Legionary actually got his own hands dirty and if any bodies are found it will look like someone else died and something else killed them. For all we know the battle on Istvaan 5 was the Alpha legion vs the Alpha legion but they just made it look like the other legions where involved and Ferrus Manus lost his head in order to troll the rest of the Imperium :).
It's not much, but here are my 2 cents.
With the word bearers its good to note 2 things. 1 they were extremely loyal to Lorgar. And 2 they were the 1st legion by a long margin to actually turn traitor, so they had plenty of time to weed out. As more of a side note, they did purge weaker parts of their legion during the battle of Calth and the shadow crusade but that's quite far past Isstvan 5.
The night lords pretty much went rogue as a legion. And I'd suggest that their actual reasoning for going heretic are fairly different than the other legions. It is noted however that in the short story Massacre by Aaron Dembski-Bowden that the Night Lords did turn on their weak/Loyal brothers whilst enroute to Isstvan 5. And they probably killed more during the dropsite massacre itself but i don't know any proof of that.
The deck gave a violent shudder at the cry of distant thunder. Broadsides, thought Talos. The Covenant of Blood was firing upon its own fleet. That, at last, made him draw breath to question what was taking place. ‘Why?’ he asked, turning to meet his sergeant’s eyes. Anrathi grinned more than most of his brothers. He did so now, bearing his elegantly filed teeth. He didn’t need to ask what the Apothecary was questioning. ‘Because I ordered it, and Captain Malcharion sanctioned it.’ ‘Why?’ Talos repeated. Irritated curiosity narrowed his eyes. He wanted answers, not another of Anrathi’s dances around semantics. ‘If we kill them now,’ the sergeant replied, ‘we don’t need to kill them later.’
The Iron warriors where quite a split legion. However, when word got out that Olympia turned heretic, Perturabo went for a mass assault on the planet millions of civilians were killed. but more notably A part of Iron Warriors resisted the orders from Perturabo seeing how crazy and cruel they where, and they were gunned down by their own battle brothers. Though the legion as a whole was really stunned at this. It quite shows what they would do for their primarch and it probably spiraled do quite fast. which is described in Perturabo's Primarch novel.
For the alpha legion I don't quite know, it's complicated. It is said that they were still loyal to the emperor, though with Alpharius disagreeing with Omegon on how to help the Imperium by siding with Horus, Alpharius more willing to sacrifice and Omegon is trying to do as little damage to the Imperium as possible. So I can't fully say what's up with them other than it's complicated....
