By default all database objects that are found to be different will be included in the synchronization script. You can exclude an object by un-checking the "Synchronize" checkbox next to it, in the comparison grid. Excluding or including an object will also affect it's dependent objects. Excluding a table, for example, excludes also its primary key, foreign keys, indexes and other dependents.
Unchecked but included! You may be surprised to see included in the synchronization script an object, that you explicitly excluded. Look under the comparison options for the option "Include Dependent Objects". When that option is ON, an included object will cause all other objects that it depends on, to be included as well, even when these other objects are excluded.
