>You can have any number of primary and secondary Geany instances open.
>With simply calling configuration save, on restart you'll get *some*
>file list...

Wait, wait. That's a *competely* different problem. You *can't* allow users to have multiple instances of application which all write to one config file. 

>If that list is from a secondary (-i) instance, it'll

>likely only contain a file or two, and you would be better with the
>list from the last normal Quit

Well, it's a flaw - in the end, it's not much "better" or "worse". How you can call Geany an IDE if it looses all the open files in all instances but the last closed one? Either it's a more like a code editor (i.e. Notepad++ - limited to one instance) or it's like a serious IDE (i.e. VS or Eclipse), which, AFAIK store the separate file list for each project.

Anyway, I don't understand how anything can be a stopper to fixing an obvious usability flaw. If it worsens usability for some rare users, it would make sense to implement an option to turn it off. But I see no reasons, why majority should suffer.