I applied for a tenure-track assistant professorship position in computer science (CS) in the US. The particular opening announcement was broad, non-specific to the subarea. In my application, I emphasized the subarea X. After applying, I inofficially found out that the CS department doesn't hire in the area X, but hires in a nearby area Y, for which I could also produce a different but still valid application. Technically, I cannot change my application documents any more or withdraw my application through the website of the hiring department. The best I could do is submit a new application using a new e-mail address. This might raise concerns on the side of the reviewing faculty, or, on the contrary, it might be considered pretty normal. Any advice on whether to submit a new application? Pro/contra arguments are welcome.
Technically, I cannot change my application documents any more or withdraw my application through the website of the hiring department.
Says who? Did you talk to a real live person about this? It's quite possible they can accept an "overwritten" re-application even if the public web interface, or what-not, doesn't support this.
The best I could do is submit a new application using a new e-mail address.
Not so. You can write a letter, explaining how you understand that the department's hiring focus is Y rather than X, while your earlier application emphasized X, and asking the application reviewers to consider an enclosed summary of your activities and plans regarding Y.
Actually, submitting again with a new email might possibly be interpreted as improper, even fraudulent. Instead, contact someone in the department that is hiring and ask for advice. Do it in person, if possible, and do it soon. Let them know that you can revise your application (offline, apparently), changing the focus. Be sure to let them know that believe that you are qualified outside the narrow scope you emphasized in your original application. They will judge, of course.
Depending on the scale of things, they may or may not be willing to let you do this, but being upfront and honest with them is better than trying to "game" a possibly flawed online application system.