Read:
http://www.webyog.com/whitepaper/Preparing…__Migration.pdf
whats is new is that from version 4.1 SQLyog imports not only data but also all sorts of indexes. That is why the ''metadata tables' must be unhidden. Did you use to use an earlier version?
You may also deselect indexes from behind the 'advanced' button of each table.
If you don't know to new Migration Tool yet, also read:
http://www.databasejournal.com/features/my…p/10897_3550146