Catalysis of the reaction: GDP-N,N'-diacetylbacillosamine + H2O = 2,4-diacetamido-2,4,6-trideoxy-alpha-D-mannopyranose + GDP + H+.
GDP-2,4-diacetamido-2,4,6-trideoxy-alpha-D-glucopyranose hydrolase/2-epimerase activity