I recently deleted a Custom endpoint via the Web console. However the custom end point is still listed in my endpoints. If I try and call the endpoint returns with a message that the endpoint is no longer there. I would like to create a new endpoint now, but I am unable to as I have hit my limit, and the system still thinks that the original endpoint is still there. Is there any way to reset it, or do something to remove it?

Have you tried refreshing the page after deleting the endpoint? It's possible that the detection of limit was not updating on deletion and would require a page refresh.

Yeah I did that a couple of times. Logged out closed the browser, etc but it stayed there. Even logged in from a different machine. After a couple of hours it did eventually disappear.