Your affidavit in 2004 is valid as the agreement of sale was entered in to on 27-06-1999 and you have been living in the house as a licensee.
Executing a sale deed is different from agreement to sell. In your case, it is the duty of the buyer to get the sale deed executed. As far as you are concerned, you have executed an agreement to sell, received the consideration and also handed over possession. so technically you are not the owner of the house since 27-06-1999.
The same having been confirmed by the court in 2010, your affidavit is legally valid and tenable.
Since FIR is quashed,, there will be no issue in closing the criminal complaint as well.