Am I not able to put the AppleID of the current podcast in the itunes settings for podPress?
You can this. But this is only for creating the iTunes URL in one of the widgets of podPress. It will not help you to submit the new URL to the iTunes server.
I still have the URL/domain of the old podcast...but the files are no longer on the server.
That makes it more complicated. One way to solve this problem is to contact Apple in order to tell them about the deprecated URL.
But you may try to create redirect which tells all requesters of the old URL that the feed has been moved permanently (see http://en.wikipedia.org/wiki/HTTP_301). If the server software is Apache then you may create a .htaccess file with the necessary commands. On other servers exists a similar possibility.