If CA Workload Automation DE R12 (DE) is using domain authentication to connect to the SQL database, then the patch must be applied by the user that starts the DE service.
Login in to the Windows server as the domain user that is used to start the service. This domain user is also used by SQL database to authenticate DE.
Note: For more details on the DE service, check the service in Services console in Windows. You can access Services console by running services.msc.
To check if the DE is utilizing domain authentication when connecting to SQL database, check db.properties in <drive:>:\<install_directory>\conf\.
The file will have JDBC URL similar to this (the following is an example): jdbc:sqlserver://SQLDBhost:1433;databaseName=dSeriesDatabaseExample;integratedSecurity=true