WELCOME TO THE BOARD!
I'm not sure if this will take care of what you are looking for, but here are a couple of stabs.
Instead of doing a WorkBook.SaveAs do a WorkBook.Save so that you won't get the prompt.
Otherwise, if you need to use the WorkBook.SaveAs, then you can try adding a SendKeys "{ENTER}" command so that the enter key is pressed/sent after the SaveAs command.
Did this help?