By default all the objects that were found to be different during the comparison of the two schemas are marked for inclusion in the synchronization script. However, you can choose to exclude or include certain objects from the comparison by un-checking/checking the "Synchronize" checkbox next to each object. Selecting or un-selecting a parent object will also affect it's dependent objects - for example, if a table is un-selected then all its primary keys, foreign keys, indexes etc. are also un-selected.
Unchecked but included! You may be surprised to see included in the synchronization script an object that you explicitly excluded. Why are those objects included? To answer this you need to look under the scripting / execution options and see if the option to "Always include dependencies of user-selected objects" is ON (default). When that option is ON then an included object will cause all the objects on which it depends to also be included in the synchronization script. For example, if you have a table T1 that contains foreign keys coming from tables T2 and T3 then, even though you may have un-checked tables T2 and T3 if T1 is checked then both T2 and T3 will be included. When the "Always include dependencies of user-selected objects" option is OFF then your object selection is respected, however, in this case you should be aware that the resulting synchronization script might not execute successfully.
