Make sure that your databases log file has enough room to grow. Altering a table that requires the table to be rebuilt requires that the log file can grow to at least the same size as the database.
If that does not work and you still get a timeout returned from the SQL Server you can use SQL Server management Studio to change the SQL Server settings;
1. In the options under "Query Execution", you can set the "Execution Timeout" there. You can set it to 0 for unlimited
2. In options under "Designers", it says "Transaction Timeout after", you can check a box and put in a value there.
If this still does not solve the issue after the upgrade is complete you may need to add the following to your database tblThread table manually running the following in SQL Server Management Studio. Run each below separately as two quires.
ALTER TABLE [DBO].[tblThread] ADD [Answer] [bit] NOT NULL DEFAULT (0)
ALTER TABLE [DBO].[tblThread] ADD [Thanks] [int] NOT NULL DEFAULT (0)