It sounds like you're referring to A/B testing entire emails rather than subject line, correct? If this is the case, you will need to update your smart campaign any time you add a test email to your send program. If you have a smart campaign set up that refers to an email that you are using in a subject line test, the name of the email will not be different so an update to your smart campaign should not be necessary (as long as you're already referencing the email in the send program).
You will also need to update your smart campaign when you create an email send program and clone an asset into that program. You will need to update your campaigns to reflect the correct email names, which as you mentioned, will change since they are now a part of a different program.
Unfortunately there is not a shortcut for auto-updating your smart campaigns when adding a test.