Hi Matt,
The schema designer is designed not to keep track of the table name changes and hence will raise error messages about tables not existing upon saving. But the bug here is that SQLyog saves the schema XML in spite of throwing the error message and this will be rectified. So henceforth if the tables are renamed/dropped after being loaded into the schema designer, SQLyog will throw an error message while saving the tables and will not save the tables as well.
Regards,
Aparna.