What I have been doing wrong with testing expunged emails, is working with 
linked copies of emails. Although thunderbird copies the message, it looks like 
the message is NOT copied but linked.

If I drag 3 emails from my desktop to a folder INBOX/test4 and copy 1 message 
from INBOX to INBOX/test4. I have 4 messages in this folder. I now shift+del 
this folder. 

The expunged messages listing gives me the expected 3 messages 

doveadm -o 
mail_location=mdbox_deleted:/home/popusers/testtest/mdbox:INDEX=/home/popindex/testtest/index
 mailbox status -u testtest 'messages vsize' '*'
Sent messages=0 vsize=0
Drafts messages=0 vsize=0
INBOX/test2 messages=0 vsize=0
Junk messages=0 vsize=0
Trash messages=0 vsize=0
test3 messages=0 vsize=0
test1 messages=0 vsize=0
RESTORED messages=0 vsize=0
INBOX messages=3 vsize=18079344

Lets recover these:
doveadm -v import -u testtest 
'mdbox_deleted:/home/popusers/testtest/mdbox:INDEX=/home/popindex/testtest/index'
 RESTORED ALL

Now I have 3 messages back, as expected. 

From an end users perspective if you delete a folder with 4 emails, you want 
your restored backup to have 4 emails, not 3 because one is already somewhere 
else in your folder/mailbox structure. 

The reason for copying an email to a different folder is that it is important. 
You do not want to loose it, and you want to be able to find it there.
It is wrong to assume that a user will notice that these emails are missing and 
should look for them elsewhere. 
Say you have folder for a court case, and you copy emails there relevant for 
the court case. How can you ever know after a restore that a few email are 
missing from the folder, and which ones.

I think it is bad this email is currently 'lost'. I rather have an option in 
dovecot that disables this hidden 'deduplication' feature. I think this should 
be the default setting also.

This current deduplication feature also is hazardous because if this one copy 
of the email gets corrupted on the storage, you have no copies left. That is 
exactly the opposite of what user wants to accomplish with creating a copy.

Feature request: disable this automatic linking of emails between mailboxes.
Feature request: set this as a default.

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