So, there are a couple of morals to this story. First, don’t trust iCloud. I don’t blame Realmac; it’s probably not their fault. I find it interesting that the data loss occurred overnight; I may have looked at my Clear list on my iPad yesterday evening, but I don’t recall doing so. If I had, I would have spotted that a list was missing. So my guess is that the data loss is due to iCloud itself.
Second, don’t use an app that doesn’t offer backups. I looked in my local folders and couldn’t find any readable files that I would have been able to recover from Time Machine backups. There’s a locally-stored .sqlite file, but it doesn’t contain the same data.
I won’t be trusting any important data to iCloud any more. I am slightly concerned about my contacts; I’ve had issues with them in the past. I know there are local and Time Machine backups that I could restore if I ever need to. But for the rest, iCloud is simply too precarious.
He used iExplorer to get the Core Data SQLite database out of his local iTunes backup.