There is no error except for the unexpected behavior of unread emails being populated in the client. In a dtrace of the ArchiveTask the following is seen that show EV recovering these soft-deleted emails:
{CArchivingAgent::processFolders:#6327} AgentDIR[Marketing Plans] - Recovering deleted items from Mailbox: [/o=AAA/ou=US/cn=Recipients/cn=john.smith
AgentDIR[Marketing Plans] - There are 446 possible messages for recovery
AgentDIR[Marketing Plans] - Message titled [Presentation notes] will be recovered
AgentDIR[Marketing Plans] - Message titled [Research results] will be recovered
...
..
.
AgentDIR[Marketing Plans] - 46 messages being recovered, 0 messages will not be recovered as they are Enterprise Vault items
AgentDIR[Marketing Plans] - There are 0 possible folders for recovery
AgentDIR[Marketing Plans] - RecoverTombstoneItems recovered messages/folders
The RecoverTombstoneItems registry key is enabled on the EV server:
HKEY_LOCAL_MACHINE\Software\Wow6432Node\KVS\Enterprise Vault\Agents
DWORD: RecoverTombstoneItems
Value: 1
Disable the RecoverTombstoneItems key by either deleting it or setting it to a value of 0.