When a geoprocessing service references a feature class in an enterprise geodatabase that is registered with ArcGIS Server, the geoprocessing service fails with the following message, "ERROR 000732: Input Features...does not exist or is not supported."
Use layers. Instead of referencing the feature class directly through the Spatial Database Engine (SDE) connection file, bring the feature class into ArcMap and use the layer that is created in the Table of Contents as the input to the tool/model/script.