Steps to Reproduce:

I understand that the command bar's recently opened suggestions are a separate feature to the recent files list in the file menu, but I'd say that:
Would love this feature! This always bites me when I rename a folder and all the Ctrl+P results fire a File Not Found error.
As a workaround though, the solution from https://github.com/Microsoft/vscode/issues/3260#issuecomment-239721770 works for me.
It is easily possible to clear the editor history of Cmp+P, just use this:

You can even remove individual entries:

Picking "Clear Recently Opened" will now also remove "recently used" from the picker.
@bpasero I verified that the Clear Editor History and remove from history properly remove editors from the quick pick history.
However clicking on Clear Recently Opened in the menu does not modify the quick open editor history. Should I reopen?
@isidorn good catch
Looks like "Clear Editor History" first becomes active on a reload? Perhaps something worth changing, that or force reload the editor. Unless I am wrong and it's only my version that does not show the changes instantly :)
Most helpful comment
It is easily possible to clear the editor history of
Cmp+P, just use this:You can even remove individual entries: