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When batch processing multiple feature classes (from shapefiles or coverages) into a single feature dataset in a geodatabase, some of the feature classes are not converted.
One or more of the input datasets have undefined projection information.
The Import to Geodatabase tools set the new (output) feature dataset's spatial reference based on the first dataset to be imported into it. If the spatial reference inherited is "unknown", other datasets with known spatial references will not be imported since it is impossible to project from a known spatial reference to an unknown spatial reference.
Make sure the first feature class in the Batch grid has a defined spatial reference.