Messages won't fully delete from icloud

I recently cleared out a ton of old messages, and switched on autodelete after thirty days to clear up some icloud space. After deleting everything, I manually synced messages in my icloud settings. It did clear up some space--messages data went from 2GB to 1.4GB, but it still says I have 47,000+ messages stored in icloud, when the only messages showing on my devices are ones I've sent in the last two weeks (and I sure didn't send 47k messages in the last two weeks). I use icloud on two devices, my iphone and my macbook air. Both devices show all the old messages having been deleted. That said, I do generally have issues getting messages (and contacts, and notes....) to sync properly--if I delete messages on my phone, I often have to manually delete them again on my laptop. Where are these 47,000 messages being stored, and why? Does anyone know how to actually delete them?