Yeah, I don't know if OpenToonz keeps track for undos on separate layers. You should ask the devs on GitHub.
Does the undo not work after you've saved (Ctrl+S)? Go to Toolbar > File > Preferences or Press Ctrl+U.
In the Preferences window, go to the Saving Tab and the last check box should be "Clear Undo History when Saving Levels." You may want to uncheck that.