We had a loan file that was closed for incompleteness. Would we select 7-Application incomplete for reason for denial?

There is a difference between the credit request being closed for incompleteness or denied for an incomplete application.

Did you deny it for being incomplete or did you send the written notice of incompleteness and the time for furnishing the requested information has expired?

They were sent a written notice and did not furnish the information. The time period expired.

In that case, you would code the Action Taken as "5" - file closed for incompleteness instead of a "3" for denied. Technically, the app is incomplete, not denied.