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The Manuscript Division at the Library of Congress has custody of the records of the U.S. Works Project Administration, which administered the Historical Records Survey. The finding aid for this collection (link to PDF) indicates that it contains administrative records for the Church Archives Inventory, in addition to correspondence, survey sheets, research notes, newspaper articles, and transcripts relating to the Church Archives Inventory for the District of Columbia. The collection does not contain the records of the Church Archives Inventory for any other state, and it does not appear likely to contain a comprehensive list of the archives for all 50 states. A more extensive search of the collection would be necessary to be certain, and you are welcome to visit the Manuscript Reading Room to conduct a search of the U.S. Works Project Administration Records.
Most, if not all, of the Historical Records Survey projects for each state published an Inventory of Church Records for their state, and these are available online through HathiTrust. See, for example, the Inventory of the Church Archives of Michigan. A guide to the unpublished inventories, indexes, and transcripts from the Historical Records Survey may also be found on HathiTrust (link), and this may assist you in determining which states produced a church archives inventory.
I hope this information is helpful. Please do not hesitate to reply if we may be of any further assistance. All the best of luck on your research project!