The server-side publishing tool copies data in the service definition file (.sd) to a server's input folder. If for some reason it can't find the input folder, the publishing process fails. This can happen if the folder was renamed or deleted after being registered with the server.
The input folder is used when you publish services and service definitions. For each service that you publish, a folder containing the GIS resource is created in the input directory. If you selected to include the data referenced by your service when publishing, the data appears within the same folder as its parent document. This input folder is necessary for the service to run properly on the ArcGIS Server site.
This server system tool is invoked by the publishing client (Manager or ArcGIS Desktop) when you create a service.
Verify that the server's input folder is correctly configured.