There are several railroads depicted on maps in the Atlas to Accompany the Official Records that did not exist. Below are the ones I've identified.
Reference Comment
A road is shown west of Richmond and west of the Richmond & Danville RR, both south and north of the James River. The road on the north side is the Tuckahoe RR (which may not have been a steam road at this time) and the road on the south side is not known to have ever existed.
The road east of Powhite Station (on the Richmond & Danville RR) and farthest from the James River had been removed in 1857. It had been the Chesterfield RR to coal mines. It is likely that the Confederate Navy had the road extended to their shipyard on the south side of the James River, but I have no document to proved it existed.
LXIII/1, 6 The road shown from Navy Cove to Fort Morgan, Mobile Bay, had been a tram road at the start of the war. It was in active use in 1861. In January, 1863, the iron rails were removed and replaced with wooden rails.
Fort Morgan Map
NA, RR 4-27-61
NA, M&O 5-1-61
NA, S&C 5-11-61
NA, M&O 9-30-61
NA, RR 10-24-61
NA, RR 10-29-61
NA, M&O 10-30-61
NA, S&C 10-19-61
NA, RR 10-31-61
NA, RR 10-31A-61
NA, RR 11-20-61
NA, S&C 12-7-61
NA, M&O 11-15-61
NA, DG 1-31-63
NA, RR 3-31-63
NA, S&C 6-15-64
CXLVII The "Mobile & Pensacola RR" was never constructed.