Applying twice for the same position 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.