As it is becoming obvious that succeeding versions of MuseScore cannot be expected to respect layout and formatting created in previous versions, a tool which would 'lock' an existing score against changes unless authorised specifically (via an 'are you sure?' or other prompt-style pop up) would be most useful.
In addition to protecting scores against unforseen changes in layout due to differing versions, a 'lock-score' tool would also help users avoid making inadvertent changes to note pitches or durations, which can be caused by a careless keystroke or movement of the mouse. Computers may be perfect, but users aren't, and we all know that something as banal as nudging a mouse while reaching for one's cup of tea can introduce unnoticed and unwanted changes.
I suggest putting it in the 'Tools' menu; that would seem to be the logical place.