SonarQube 6.0 is the last version to support MS SQL 2008. See: SONAR-7893 - End of support of MSSQL 2008 Closed
SonarQube now manages secure flag on Cookies
So far, if you were securing your SonarQube server behind a reverse-proxy, you had to make sure that Cookies were marked as secure at proxy level. Starting from v6.3, SonarQube automatically sets that flag when interacting via HTTPS. You should therefore remove any custom config you would have put in your reverse-proxy to flag SonarQube cookies as secure.
The data migration performed during the upgrade to SonarQube 6.0 induces high fragmentation on some of the tables. On big databases, this can impact performances of SonarQube. As documented on the Upgrading page, this is highly recommended to refresh your database's statistics and rebuild your database's indices once the technical upgrade is done.