Are you sure you are trying to reproduce it correctly?
Maybe I didn't describe the reproduction steps in enough details - in (2) you have to switch to another window (e.g. terminal containing`vi`) and after you modify the document there, the click inside Geany's editor must be the one by which Geany gains focus (i.e. do not first click in Geany's title bar to get it in the foreground and then inside Scintilla).