In general, you can not modify a secondary database directly. In order to modify a secondary database, you should modify the primary database and simply allow JE to manage the secondary modifications for you.

However, as a convenience, you can delete SecondaryDatabase records directly. Doing so causes the associated primary key/data pair to be deleted. This in turn causes JE to delete all SecondaryDatabase records that reference the primary record.

You can use the SecondaryDatabase.delete() method to delete a secondary database record. Note that if your SecondaryDatabase contains duplicate records, then deleting a record from the set of duplicates causes all of the duplicates to be deleted as well.

For example:

package je.gettingStarted;

import com.sleepycat.je.DatabaseEntry;
import com.sleepycat.je.DatabaseException;
import com.sleepycat.je.OperationStatus;
import com.sleepycat.je.SecondaryDatabase;

...
try {
    // Omitting all database and environment opens
    ...

    String searchName = "John Doe";
    DatabaseEntry searchKey = 
        new DatabaseEntry(searchName.getBytes("UTF-8"));

    // Delete the first secondary record that uses "John Doe" as
    // a key. This causes the primary record referenced by this secondary
    // record to be deleted.
    OperationStatus retVal = mySecondaryDatabase.delete(null, searchKey);
} catch (Exception e) {
    // Exception handling goes here
}