You can control what appears in the popup menu by using a cell array containing the strings you want to display.
For instance you don't have to clear the existing popup menu's content but rather replace it with what you want:
MyStrings = {'5' '4'};
set(handlesToPopupMenu,'String',MyStrings);
and it should update correctly. If on the other hand you want to retrieve the content of the popup menu as a cell array, use this:
MyStrings = cellstr(get(handlesToPopupMenu,'String'));