if you try to synchronize the same table in two databases and you've added one field, one index and one foreign key to one table The Structure Synchronization Tool will not copy the foreign key.
I'm using InnoDB tables with MySQL 4.0.18 on Win2000.
I would be really cool if you could add this feature. This is the only one that is stopping from doing a full structure sync. I am enjoying using SQLyog and would recommend it to everybody, I am going to remmend my company to buy more licenses of this product.