Trying to upgrade SQL Server 2005 Express might not be an easy process. First, there are different files for standard version and Express versions – and there are different files for Express and Express with advanced services. And, the Express upgrades are not really upgrades at all – but the full install. When you run the full install against an existing copy, you get the option to upgrade.
WSUS can also push these upgrades down to your machines. In some cases, this worked and in others I always got the very helpful 2259 error – “The installer has encountered an unexpected error. The error code is 2259. Database: Table(s) update failed”. Also got this error when running the ‘update’ directly (not from WSUS) while following the readme instructions exactly. There seems to be quite a few instances where this error occurs, but precious little information about what the solution actually is.
In my case, the only solution was to install a new instance along-side the old instance. Move the user accounts over (kb article 246133), then detach databases from the old instance and attach them to the new instance. Then update and web.config files accordingly.