Messages in custom folders are not getting archived. Here is a reference article if you want to learn how to Manage LoopMail.
This issue is typically reported by students or teachers who use the Loopmail. The messages in Loopmail are archived at the end of the school year into the respective archive folders.
Messages in custom folders remain in the respective custom folders. Only the messages in the folders like Inbox, Sent and Current Archive messages are moved to the Historical Archives. This process is automatically triggered at the end of the school year. There is a new Historical Archive folder created for every school year in the past.
Custom folders do not have a historical Archive folder.