Insider v0.16.3. 3rd party plug-ins were not disabled before testing, so you can ignore this, but I am going to keep it in case anyone else is experiencing anything similar since it is pretty annoying.
I was editing the daily note on my Windows Desktop, had it open, then opened the mobile app for iOS (insider version again) that opened the same daily note and after syncing finished, the app only saved whatever I had in my daily note on my mobile device as the latest version. I restored the correct version via the note sync version history feature.
I was able to reproduce the issue hours later when opening Obsidian on my Macbook. After syncing was complete, my Daily Note wasn’t overwritten with the latest changes. This time I had the Windows desktop app and mobile app closed.
The one thing they shared in common is that I moved several files into a different folder, so Obsidian had to delete and re-download about several hundred files in the background while the daily note was open, but didn’t overwrite the daily note. The sync status was set to green on windows desktop, so it’s not like there was an issue there.
I use templates for my daily note using the core templates plug-in and the template is what was set as the latest note each time.
This is not the same issue as when opening a vault, in v0.15.9 of a Windows desktop app that doesn’t use sync or a cloud storage folder, the daily note is completely cleared out on startup if you use an pinned Obsidian URL shortcut to open Obsidian vaults through the taskbar.