It's the only bit that I found confusing. It took me a while to put everything straight. I suspect it may be in part due to the fact Jordan had planned Mat to arrive in Caemlyn later than Brandon had him, and some elements (like the rumours about the Tower reunification, real in Jordan's mind, but made false by Brandon's timeline) have not been smoothed out clearly enough.

But it's clear though, with a bit of work. Brandon said last year Mat was about 30 days behind Egwene and Rand. He was in Caemlyn only for a few days in his first chapter in TOM, so weeks before the reunification and the epiphany. He sent his second letter to Elayne shortly after, and they met. That was still weeks before Elayne and Egwene met post reunification.

Most of Elayne's storyline (securing the Kin, the battle in the dungeons etc.) takes place before she meets Egwene. Her taking of the Sun Throne is one event which clearly takes place after her meeting with Egwene, and shortly before the meeting with Rand north. Gawyn's visits too, a bit earlier. Perrin and Galad she had already met when she visited Egwene, so she could tell her the WK will fight with AS etc.

So yeah, when Egwene and Elayne met and she was told about the BA purge, Elayne didn't have any BA prisoners anymore. They were dead or escaped. Brandon didn't want to spoil Elayne's storyline (and her meeting of Galad, Perrin etc.), that's why he had her give Egwene all her news behind-the-scenes only, and that's why Egwene conveniently never thinks in her POV about the developments in Caemlyn.

That's one example of how I found TOM messy. Important developments were just swept away to avoid "spoilers", and didn't have the impact they should have had, at Brandon put the chapters in a more chronological order (I don't really see what showing Egwene early in TOM really brought. The fact Rand was to break the seals was "artificial suspense", that was a poor substitute for "Rand's darkness"., because few readers are alarmed by the fact Rand wishes to break the seals - most side with him against Egwene's POV...) Brandon had painted himself in a corner by showing the epiphany too early before it happened on Perrin's, Mat's, Elayne's, Aviendha's timelines. He made the same mistake RJ did by showing the Cleansing first, then returning to the weeks before in COT. Brandon had no choice to do this, because Perrin was to confront Mesaana with Egwene, so Egwene had to appear early to provide a build up to the event. I'm convinced in RJ's outline, the confrontation with Mesaana happened as Egwene purged the BA. Perrin came to TV in his fight with Slayer, Mesaana went down, and Perrin saw Rand on DM).

Mat was cornered by Elayne, and she intended to find the truth about his wedding at dinner. Between him, Talmanes and Thom, we can suppose she succeeded. This means she almost certainly told Egwene about Mat's ties to the DOTNM, especially after Egwene told her of the Seanchan attack. Elayne never really shows a reaction to the Seanchan attack, even if her scenes after she's met Egwene. It should have alarmed her quite a bit. Mat never shows any sign Elayne told him his wife attacked Egwene either - and that should have created a shock for him.

The way Brandon wrote all this is ambiguous. It appears Elayne has not learned the truth about Tuon and Mat, but it was a poor choice to foreshadow that she would get the truth of it from Mat at a behind-the-scenes dinner, and then never return to this topic in the book... It sounds like Brandon put a hook for this when he wrote the Mat chapter, and then forgot it was there when he wrote the Elayne parts (they were not in the same POV cluster).