Since v10.2 there is an additional option in the domain called "Samples only". If you set this to "Yes" only objects labeled as samples will be considered in the execution of the process.

For example you can save your Samples as a temporary vector file in the project as a backup using the "convert image objects to vector objects" algorithm and simply setting "Samples Only" to "Yes". Adding  the "Sample Class name" attribute to the Attribute table and you are good to go!

Afterwards, you always can fall back to your sample backup in form of the vector and restore them, even though your image objects might have been destroyed! Very cool!