I encountered a weird thing in the scope of this subject today, using MacOS Sierra:

MoI worked fine so far since my Sierra upgrade, but this morning when I started MoI, a Wine dialog appeared, presenting a number of installation options, as if I had just installed Wine and now needed to manually install MoI from the Wine UI.

I never saw the Wine dialog before, I just knew in the back of my head that Wine is used as a container to run MoI on the Mac.

What I did (as I don't know anything about Wine) is:

1: copied my custom commands from the Commands folder via Show Package Contents,
2: deinstalled MoI,
3: downloaded it again from the site,
4: reinstalled it,
5: copied back my custom commands.

Everything works fine again now. As I had not removed the license(s) or the Moi.ini file, that wasn't necessary to copy back.