The bottom line is this. To qualify for the capital gains exception, you must have lived in it for 2 of the last five years, counting backwards from the closing date on the HUD-1 statement you will receive at the closing when you sell it. What you can do is select the option for 2 of last 5. The program will ask you for days lived in, in the last 1826 days prior to the closing date. If you qualify for exceptions that allow pro-rating, the program will know "BASED ON THE DATA YOU PHYSICALY ENTER". If you don't qualify, you don't qualify.
There are exceptions for active duty military who are moved under orders. But those exceptions allow for extension of the 5 year rule, and not for a reduction of the two year rule.
