A few months ago the developer of Notebooks posted on this forum and said, “We started implementing and experimenting with iCloud sync a couple of years ago, but the user experience is not at all what we want. When syncing huge hierarchies of documents, you have no idea about the progress, the process may even stall and maybe continue, or not. Sometimes iCloud thinks that a book/folder has disappeared, so that book disappears from Notebooks as well, just to reappear a few moments or minutes later (the same can happen in Apple’s Calendar, by the way, and even when syncing folders between two Macs via iCloud). This is not the type of sync we want in Notebooks.”
Sadly, this is not the first time I’ve heard this about iCloud sync, and it explains why some apps choose to sync with Dropbox over iCloud. It’s too bad that Keep It does not offer altrernative cloud-sync options.