As a workaround, try doing a 'Save As..' rather than a 'Save' (in fact, when I am editing an existing text file in QMIDI, the 'Save' dialog is greyed out and only 'Save As' is available). Make sure the original file is the name (it should be unless you change it).
Then you should see the dialog box
and you can accept the overwrite.
EDIT: I just read your OP, and it appears you are first selecting another file, THEN doing the save of the one you were just working on. It might be that this is your issue. Perhaps something has changed in the latest High Sierra update (were you running that before the problem started?) that doesn't allow you to overwrite a file as you load another one?
If you change your workflow to saving the edited file BEFORE you load the new one, I think you should get that overwrite dialog box and be able to save with the same name. That's how it works on my system, at least...