Churches are not required to obtain an official recognition of exemption to be exempt from income tax and to be able to accept deductible charitable contributions. Therefore, it would appear that you don’t have to file to be an exempt (c)(3) organization if you meet the IRS definition of a “church.” (See Ready Reference Page: “What Constitutes ‘Church’ Eligible for Exemption?”) Many churches do file to obtain the recognition letter in order to have the piece of paper to show anyone who asks.  I assume that your denomination will remove your church from its list, but that doesn't mean that you necessarily have to do anything if you still meet the IRS definition of a church.