Our apologies, these instructions are for AutoMate Pro/Premium.
Sounds like you have Enterprise. For Enterprise, all of your workflows, tasks, settings, etc.... are all stored within your database. You would need to create a backup of your database via SQL management studio (or something similar).
From there you would install the software via advanced install. When it comes time to select the database, select "Existing SQL Server, MySQL, Oracle or OLEDB database ". Then, you would enter the credentials to reconnect to the database. Obviously you will need a network connection from the database machine to the AutoMate machine.
If there is an issue with the database, you can restore the database you created and attempt to connect again.