I applied for my wife's itin with federal tax return in January end and I also filed state taxes paper based leaving the ssn/itin area empty.

I have received the ITIN number today.

My question is I have not received the state return yet and it has been just 3-4 weeks since I filed mailed paper based CA state tax.

Now that I have received her ITIN number can I efile my state tax and get my refund early. What will happen to my paper based income tax that I filed in January end?

Will it be ignored or create any problems?

In the past, California HAS processed tax returns which have ITIN applications pending with the understanding that you would forward a copy of the ITIN letter to them at a later date.

It is possible that the Franchise Tax Board has changed that position. You need to call the California Franchise Tax Board and ASK about the status of your return.