First, thank you for the comprehensive report with all the information we 
normally have to ask for.

You noted that this has been the behaviour of Geany projects for some time.  
That is because it is the intended behaviour.  You see, a Geany "project" is 
nothing much more than a named session file, it keeps a list of a few settings 
and the files open.  Therefore if a file in the list does not open it _should_ 
be removed from the list.

So a Geany "project" is not like projects in Visual studio and some other IDEs 
where they need to know all files in the "project" to provide some extra 
functionality, like symbol management or build management.  To get something 
like those sorts of functionality you can try the project plugins (there are 
several).

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