The same objects that have different owners or schemas are treated by Schema Compare as different objects. For instance, if a stored procedure exists in both databases and is identical except for its owner, it will be considered as a completely different object.
If you want to compare objects that are the same but have different owners, you can remap the owners when you set up your comparison project.
You can not compare extended stored procedures with the Schema Compare tool.
You can decrypt text objects databases created using the Decrypt encrypted objects option.
When this option is enabled, the Schema Compare tool decrypts bodies of encrypted objects for comparison and synchronization. They are shown in the comparison results as usual script objects. If you compare encrypted objects in databases with large amounts of data, selecting this option may slightly slow down the comparison.
As SQL Server restricts access to logins, certificates, and asymmetric keys, Schema Compare can’t compare all of the properties for a symmetric key.
To ignore all logins, certificates, and asymmetric keys in the synchronization, on the Options tab of the New Schema Comparison wizard, select the common option Ignore logins, certificates, asymmetric keys for users.