I know this is old, but it's still a top search result. I found an awkward way to do it (for pycharm anyway) when I got a file stuck in my switcher list that had the same name as a project file and it was REALLY irritating.

Go to the "System directory" for whichever product (%LOCALAPPDATA%\JetBrains<product>) and in the "workspace" directory there are some randomly named xml files. One of them contained "<entry file=..." elements for the files I wanted to remove from my switcher, deleted those, restarted pycharm.