The IRS uses Notice CP88 to inform you they are holding your tax refund until you file. This is essentially the same Notice as the CP63. The IRS believes you owe taxes or they would not have sent Notice CP88.
Confusion over Notice CP88
A lot of times, people believe that they did file but the IRS says otherwise. If you have the certified mailing receipt showing the IRS stamp then you can argue about the filing date and there is a procedure for doing that. But, absent the mailing receipt, it is usually better to just re-file than argue. It isn't going to make a lot of difference in the final outcome & they must be filed anyway. However, since you are filing an original return you are allowed to go through your records and find more deductions before filing!
Often, people fear that the documents needed to prepare the returns are lost. This law office specializes in finding and reconstructing lost records. See Lost Documents.
This IRS Notice CP88 is NOT an audit & will likely not become an audit. The IRS just wants your returns. But, they have evidence that you owe so you have to be careful.
The IRS can't enforce collection against you until you file a return or they file one for you. So, you have time to correctly prepare the returns. It's best to investigate your case carefully.
Because of the legal and procedural implications, it is not necessarily wise to rush out & file returns, especially if you owe. We need to get the IRS file and create an Action Plan for your specific situation. Please follow the Prep Steps for IRS Notice CP88 and see Mr. Hopkins in Denver, Pueblo or Colorado Springs before you file!