I have discovered another variant of this problem:
When trying to compile finalized code, a pop-up says it couldn't create the F-Code directory (see screen shot). While the pop-up was still open, Windows explorer saw the F-Code directory already (see screen shot)!
To add more surprise to this problem:  When I used "Alt+F8: Find added classes and recompile" it worked, and after that compiling the finalized system also worked! It looks very much like an obscure bug to me; at least the error message pop-up is not telling the truth. Reliable software should not lie!
I'd also wish there were some event log of EiffelStudio to help debugging this.