Churches, including synagogues, mosques and other religious worship organizations, local units of churches, conventions or associations of churches, and integrated auxiliaries of churches are not required to file the Form 1023 application for recognition of exemption in order to be exempt from federal income tax under Section 501(c)(3), although many do file so that they have the exemption letter to show to potential donors. The same groups are also exempt from filing the annual Form 990 tax return, although they must pay unrelated business income tax if they have any.  So the direct answer to your questino is that there are no implications from failing to obtain recognition of exemption.