I could tell the program to "find all the Eb3's in this staff and select them" (use the select staff menu popup to prompt me for a staff to choose).
The result would be all Eb3's in the staff selected. I could then use the semitone down button to lower the notes to D3.
A shortcut to this could be to let us select a note (I select Eb) and then in the Score menu, have an option "Find notes like this..." and in the parent staff of the selected note, the program would select all the notes that match (in the same octave, an Eb4 wouldn't be selected if a Eb3 was used to start the search).
I think a feature like this would also be great for adding/removing accidentals, especially after using the semitone up/semitone down buttons on a group of notes/bar/staff.