I am just curious is there a specific process I need to follow when I want to decommission either a single BES 4.1.6 server or the entire infrastructure.

I am asking this because I am preparing for a 5.0 install and will be setting up a new database and migrating the users to all new servers using the transport tool and want to remove the old servers when I am done.

I know temporarily as I remove all the users from a server I can turn the BES services off. But I want to know if there is anything I need to do to retire them and the infrastructure completely once I am done with the migration.

Thank you in advance for any advice you can give me.

Removing the BlackBerry Enterprise Server or BlackBerry components for a decommissioned BlackBerry Enterprise Server
KB12429 - View Document

I saw that document earlier and thought that would be good if I was removing one server from a 4.1.6 BES domain. But what about when I am on the last server to remove? Once I remove it is that 4.1.6 domain completely gone then?

AFAIK, if this is the last server in the domain and the DB, you can just shut it down. As a last step, you can delete the corresponding SQL DB and the service user (if you are using a different one for the new 5.0 domain).