I’ve never heard of it either. But the SBC cannot, CANNOT, tell individual churches what to do. They have independent authority.
What makes this Ironic is that the Battle Flag of the Army of Northern Virginia deliberately incorporated the Scottish Saltire as it's main theme. In other words, it's a Christian Cross that is it's primary symbol, like the flags of many nations of Europe.
Historic Episcopalian churches, like the National Cathedral in Washington DC and St. Paul's in Richmond, do have representations of the confederate battle flag in stained glass windows, on plaques, in woodwork, and in books, and they're trying to get rid of those images. I'd be surprised if they actually had the CBF flying there on a regular basis.