The Managed Folder Assistant, a mailbox assistant that runs on Mailbox servers, processes mailboxes that have a retention policy applied.
The Managed Folder Assistant applies the retention policy by inspecting items in the mailbox and determining whether they're subject to retention. It then stamps items subject to retention with the appropriate retention tags and takes the specified retention action on items past their retention age.
The Managed Folder Assistant is a throttle-based assistant. Throttle-based assistants are always running and don't need to be scheduled. The system resources they can consume are throttled. You can configure the Managed Folder Assistant to process all mailboxes on a Mailbox server within a certain period (known as a work cycle). Additionally, at a specified interval (known as the work cycle checkpoint), the assistant refreshes the list of mailboxes to be processed. During the refresh, the assistant adds newly created or moved mailboxes to the queue. It also reprioritizes existing mailboxes that haven't been processed successfully due to failures and moves them higher in the queue so they can be processed during the same work cycle.
Based on your description, I assume all mail items are moved to the "archive" after 1 year (365 days) and then permanently deleted after 3 years (1095 days). Is this correct?
Again, I assume you want no mail items older than 3 years in any mailboxes (regular or archive) that have the retention policy assigned.
If my assumptions are correct, then the retention tag to delete all mail items older than 3 years will not effect the "regular" mailbox but only what is in the "archive" as the "regular" mailbox should not have any mail items older than 1 year in it.
Am I understanding you correctly?
Unfortunately, the retention tags do not allow us to target folders only in the "archive", and we are unable to assign multiple retention policies to a mailbox or a separate retention policy to target the "archive" specifically.
I hope this helps.