I have had a similar experience with Obsidian notes. I would edit the “today” note at different times on my computer and phone, and noticed that I lost content. This seems to happen most when I started a note on my computer, then opened it on my phone. Obsidian has a loading screen that seems to imply that the file system successfully got the latest updates from iCloud, but perhaps it didn’t actually have the latest updates as I started writing.

I recently switched my Obsidian notes off of iCloud. I’m using their hosted sync service, and expected to be better – but don’t have enough experience with it yet to be able to recommend it.