We may have seen x-iel or at least his host, the Fallen can keep hidden especially well, Harry may have fought him and not even realised he was facing a Denarian, Cowl for example is a likely candidate, he never pressed Cowl hard enough for him to draw on Hellfire in their battles. Cowl however knew Harry possessed Bob, who had the Word, if Justin was a previous host x-iel would know this. It always bothered me that Cowl knew about Bob when only Justin, Elaine and Harry knew this, so Cowl must have found out from Elaine, unless there was another being present all the time. Everyone goes with the Elaine-Kumori theory, but if she was bound to Summer at the time of Grave Peril, it’s unlikely given how we have subsequently seen how Winter binds.
It's possible, but not the only way to explain Cowl knowing Justin had Bob and surmising Harry would have taken the skull after defeating Justin.
We have little to no indication in text how much information Justin was sharing with other Circle conspirators without Harry or Elaine's awareness. It could be something as simple as Cowl knew because he helped Justin purloin the valuable assistant spirit out of Kemmler's lab while convincing the Council it had been destroyed. That's a particularly credible alternative if Cowl is Simon - everyone pretty much would have believed Bob was destroyed on his report as Senior Councilor and head of the brute squad.
Of course, Cowl could be both Simon AND hosting one of the Denarians everybody thought was still in a Church vault somewhere. A coin would certainly be helpful in faking one's death.