Sometimes databases are set up such that each schema is supposed to have the same objects, defined in the same way, as all the others. Ex: SchemaA.Table1, SchemaA.Table2, SchemaB.Table1, SchemaB.Table2, SchemaC.... This is used as an alternative to multiple databases. Unfortunately, not all objects are always set up the same and thus the need to compare them.

SQL Compare will let you compare a database to itself, and you can use the "Owner mapping" tab to cross the schema names (e.g. map side 1 SchemaA to side 2 SchemaB), but the comparison has to go in both directions (also map side 1 SchemaB to side 2 SchemaA) or it will fail. If you do remap the schemas, then you get essentially duplicate records of changed objects because you're doing the comparisons twice.

It would be nice if you could either exclude the second half of owner mapping without errors or be able to filter each side individually so that you can effectively compare a database to itself on different schemas.