As Austin explains there is no way of prohibiting this in the modeler.
What you could do however is publish the app or module in your private appstore. All other project specific functionality should then be created in different non appstore modules. You should then agree on not editting your private appstore content(as is a best practice). See also: https://docs.mendix.com/community/app-store/
I don't think there is that option in the modeler. If any of these microflows or entities were modified, you could always use reverse merge changes to undo the changes.