code: public void dropRTreeIndex(String tableName, String geometryColumnName) {
  
  		String sqlName = GeoPackageProperties.getProperty(SQL_PROPERTY,
  				DROP_PROPERTY);
  		try {
  			executeSQL(sqlName, tableName, geometryColumnName);
  		} catch (Exception e) {
  			// If no rtree module, try to delete manually
  			if (e.getMessage().indexOf("no such module: rtree") > -1) {
  				sqlName = GeoPackageProperties.getProperty(SQL_PROPERTY,
  						DROP_FORCE_PROPERTY);
  				executeSQL(sqlName, tableName, geometryColumnName);
  			} else {
  				throw e;
  			}
  		}
  
  	}
docs: Drop the RTree Index Virtual Table
  
  @param tableName
  table name
  @param geometryColumnName
  geometry column name