Have you tried the syntaxx as below?
c:\Program Files\Wanova\Mirage Management Server>Wanova.Server.Tools.exe ExportLayers -172.16.50.40 export.csv -outputFolder 1,1.0 d:\Export
"C:\Program Files\Wanova\Mirage Management Server\Wanova.Server.Tools.exe" ExportLayers
Usage: ExportLayers
-serverAddress [Management Server address]
-layersFile [layers .csv file. File Format:
LayerId,LayerVersion ]
File format example:
#LayerId,LayerVersion
1,1.0
2,2.3
-outputFolder