Some time ago I ran into a problem while exporting/importing the Lync Configuration Store. When importing the configuration file the Lync edge server complains that the file contains corrupted data. After some troubleshooting I found that the solution was very easy, you must enter the .ZIP extension when exporting the data to the file. Otherwise it says the file contains corrupted data.
You could use the following command to export your Configuration Store data:
Export-CsConfiguration -FileName C:\LyncConfigFile.zip