Is there a way to clean Project Assistant/Recent file window?
Where are those shortcuts located?

I don’t think there is a convenient way. I just rename my main directory where the files are located. Then open the files I want to remove. It says something like “cannot find file - want to remove from list?”

Regards, Karel.

Shortcuts? Shortcut for what?

Close Cubase, rename or move the folder(s) that house the projects in the Recent file window, launch Cubase (files are gone) and then you can rename (or move) those folders back.