I just can't see Kellhus not finding a use for them. Any use. Even just tools or breeding stock. He clearly has need of things he can bonk successfully enough to make babies. He needs people who can manipulate others for him at a lower level when he's not around. He needs assassins. He needs spies. He needs guards (for important dudes). He needs people that can see skinspies. He needs sorcerers and being the Few seems to be genetic...so some surely must be good candidates. I just can't imagine him being so...unimaginative as to go in and kill everyone and blow everything up. Maybe he took the useful ones and destroyed the rest.
I definitely think he'd have gone back there at some point. It just doesn't make sense for him not to for any of the reasons I listed or more. He needs to make babies above all else and it's pretty hard for him...and there's far more mundane uses for some weaker Dunyain. He just needs to convince them he's totally awesome at the logos and they'd never even think to betray him. There's also a few characters here and there that might be Dunyain and acting out his will as it is.
That leaves me to believe the Consult found it and smashed it so Kellhus couldn't do it first. It wouldn't take much really. No matter how amazing Dunyain are at fighting or bullshitting, they can't really do much against even just a couple of sorcerers without chorae. If they even had any chorae somehow (killing invading sranc?), they'd probably be totally ignorant as to its use. I wouldn't rule out the Consult breaking a few of them and using them for their own games but still, I think they'd just wreck it if they found it. If not them then who? A raving Erratic that just happened to show up?
I think the scroll being opened hints at a very specific person finding it. If it was the Consult, they'd probably either take it with them, rape someone with it or both. Also if the Consult found the scroll, why'd they not let Wutteat out to cause some trouble for the Ordeal? They're gathering up yokes of sranc, why not have a badass zombie dragon? I don't think it could have been them. Why would Big Moe or Kellhus need the map anyway? Surely their memory is good enough to find the way home? If not, there's always magic or tracking skills to figure it out. Who else even knows about the library? Who else even knows about the Dunyain? I thought originally it could have been Cnaiür but I still think he died in the mansion way back when. If he was working with the Consult though...the above points come into play. He's the only person for me that isn't really the Consult but who even knows of the Dunyain. I just can't think of anyone else that makes sense. It could be the case has nothing to do with the destruction of the monastery. At this point I still think it's a random Erratic that felt like being a dick and there's nothing big and meaningful to it at all.