We think the problem where the layout is messed up, hiding things, may have also caused other side effects. It’s possible that saving of the data was also affected.
We should have a new beta ready in a day or two. It would be great if you could give that a try, and see if the issues stop occurring. To get the Mac beta, you just need to use the web site version, and turn on the beta stream in Agenda > Preferences.
Note also that this cropping of content problem can lead to different issues. It can lead the note text to be cropped at the top or the bottom. Imagine you see just a single list item in a note, and think most of the note is gone. It could be that the note text is hidden above. Or, if you see a list item, and think the sentence is gone, it could be a different list item, and the actual text is hidden above or below. Until we have the fix, best to restart the app when you see something odd.
(There is actually a separate bug, which we just fixed now, where an empty line can become an empty checklist. This could also contribute to confusion. Eg. “Is that one of my checklist items, and the text has gone missing?” or “Is that an empty line that has become a check list item, and my other checklist items are actually invisible due to the cropping issue?” In short, it is an unfortunate combination of two bugs that may be causing this.)