If you’ve got the properties for the store set to never delete mailboxes or items until the store has been backed up, I believe those emails will continue to exist in the store/mailbox. Perhaps this is the reason why you can still find these deleted emails.
It seems you’re performing brick-level backups. Perhaps you should try backing up the store first, to clear out all those emails before continuing your brick-level backup jobs.
Let me know if you have any follow-up questions.
if you want to access specific mailbox you have to use xmerge to export that specific mailbox edit whatever you need then imported back using xmerge as well