Hi, this is a quick follow-up that I finally just followed the steps you suggested.
First, I made a backup of the good iPad data (I also transferred a copy of that iCloud backup to my Mac local drive, just in case).
Second, I enabled iCloud Sync on all devices (I have only one active iCloud account, so no confusion there). The Mac and iPhone were already set to sync on iCloud, so this was simply a matter of toggling the iPad to sync once again on iCloud instead of Dropbox. On sync, the iPad downloaded the auto-generated "My first diary entry" on January 1, but fortunately did not delete the other entries from that day and the end of December. The Mac also synced properly, after I pressed the Sync icon on the lower left. Finally, the iPhone synced properly, immediately upon opening the app.
I deleted the auto-generated "My first diary entry" and that change was recognized by all three systems.
I still don't know what was going on with the bad sync behavior earlier. I guess those are the risks of depending on cloud storage. I'm the sort of person who uses POP on my laptop so that my email messages get stored locally and are subsequently archived. I'll probably make occasional backups of my Diarium data and store them locally too.
As for end-to-end encryption, I'll just let iCloud handle it for now, although I'll be happy when it's handled by default within the app.
Thank you very much for your help!