Currently, custom flags for moderator attention are not automatically invalidated (marked helpful) when a post gets deleted. Ordinarily, one can retract a moderator flag by going to the post, clicking "flag", and then "Retract Flag". This works even if the post has been deleted, provided they can see the post (they have 10,000+ rep, it's their own post, or they have answered it).
However, it's not possible to self-remove a flag on a deleted post if they can't see the deleted post, because they can't get to the "flag" button. Is this intended? If not, can this ability please be implemented?
As Aurora0001 commented, there is no server-side check, the button is just not visible. Can this please be implemented on the website, or is the fact that it's possible server-side a bug that will soon be fixed by removing it?