Если вы знаете набор id характеристик, которые надо удалить, то нужно выполнить следующие запросы:
delete from shop_feature where id in(1,2,3,...);
delete from shop_feature_values_color where feature_id in(1,2,3,...);
delete from shop_feature_values_dimension where feature_id in(1,2,3,...);
delete from shop_feature_values_double where feature_id in(1,2,3,...);
delete from shop_feature_values_range where feature_id in(1,2,3,...);
delete from shop_feature_values_text where feature_id in(1,2,3,...);
delete from shop_feature_values_varchar where feature_id in(1,2,3,...);
delete from shop_product_features where feature_id in(1,2,3,...);
delete from shop_product_features_selectable where feature_id in(1,2,3,...);
delete from shop_type_features where feature_id in(1,2,3,...);
Вместо 1,2,3,... подставить свой набор id характеристик.
! Перед выполнением запросов сделать бэкап таблиц !