I just noticed that the Edit>undo doesn't undo checking a to do item.
Any chance it could? The use case is when looking at all notes with the to dos at the top. If you have hide completed items turned on, then they disappear instantly. Turning that hide feature off still doesn't seem to show what you just checked. It's super easy to check something accidentally, especially when using touch.
There is (and in 2.79 also have been) two Undo handling behaviors, which can be triggered using the Global Undo property in the Preferences. Go to your Preferences, navigate to Editing, and make sure Global Undo is checked there to get back to the undo behavior.