Performance issues with SQL Data Compare

If you are stuck during deploying, you may want to save the deployment script to a file, copy it over to the target SQL Server and run it locally using a SQL query utility such as Management Studio. You can save the script by selecting 'save script' on the last stage of the Deployment Wizard instead of clicking Deploy Now. If the deployment script is too large to manage, you can select a subset of rows to deploy at a time.
You can also review the options for comparison behaviors like filtering the data (you compare only the data you're really interested in and the size of the temporary files is reduced), clear the Show identical values in results check box and if you are comparing tables with large amounts of data that changes infrequently, or select the Use checksum comparison.

If you are using professional edition of the tool, you can consider using the command line interface to create a comparison and deployment task and schedule it to run at a time when the SQL server is experiencing least activity.