CiviCRM Community Forums (archive)

But when I use mysql diff tool to compare the table structure with the database from a fresh 1.9 install, there are many differences. Is it correct?

I don't know the exact answer to this, but I would say if you are not seeing any errors while using CiviCRM that it worked. Between 1.7 and 1.9 is 2 big releases, and there are always database changes, so it doesn't sound out of place that the table structure is different. Just check the functionality of CiviCRM and make sure you are not getting any errors. Also, 1.9 was primarily a CiviMail upgrade, so check out CiviMail (if you're using it) and make sure that you see the new functionality. I believe that is the version where they added the ability to compose your mailing right in the page.

Then I tried to update 1.9 to 2.04, but I didn't find civicrm_41.mysql. Where can I find this file?

You should try to do the upgrade through the web browser -- they added this functionality in the 2.0 release so you don't have to use the mysql source command. The upgrade instructions from 1.9 to 2.0 are different than the previous version upgrades.
You did not specify if you are on Drupal or Joomla, so I will give you both options:

If you are on Drupal, the upgrade page is here: http://wiki.civicrm.org/confluence/display/CRMDOC/Upgrade+Drupal+Sites+to+2.0

If you are on Joomla, the upgrade instructions are here: http://wiki.civicrm.org/confluence/display/CRMDOC/Upgrade+Drupal+Sites+to+2.0

Hope that helps.