Mail retention - storage of potential duplicate Data

There are no files, everything is stored in place, within the mailbox itself. Moving items within the mailbox itself, including to/from any associated archive, does not affect storage. Moving data between mailboxes, or to Groups/Public folders will result in a copy of any moved item being preserved for the duration of the matching retention policy.

In other words, if the mailbox is under (generic/blanket) retention policy, all data within is preserved, regardless of any deletions/moves. This is why "cleanup" operations require you to (temporary) disable the retention policy, see for example https://learn.microsoft.com/en-us/exchange/policy-and-compliance/recoverable-items-folder/clean-up-deleted-items 

Nowadays, we do have the Priority cleanup feature as well, which can help in such scenarios.