Here is the test case :
I have filtered ALL my inboxes so that all incoming Emails will go into an unique local folder.
Test case :
Send 1 Email with to my first address AND second address both as recipients.
2 (same Emails) arrive to my inbox (from my two addresses).
Expected result :
If I reply on the first one, it shall go from my first address.
If I reply from the second one, it shall go from my second address.
Observed result :
If I reply from any of them, it will go from the first address.
You haven't stated what your filtering rules are, and their order. Please do that.
Here is my filtering :
On Menu :
"Configuration" > "Edit Accounts" > my_first_email 
Go to :
"Account" > "Receive" > POP3 section :
[ ] Use authentication (APOP)
[ ] Delete messagees from server when receiving them
Delete after 1 day 0 hours
[ ] Limit size when receving [greyed out] kb
Entry by default #/Mail/inbox [Button Explore]
[X] Filter messages when receiving
[X] Enable filtering using plugins when receiving
[X] "Receiving Email" check if there are new messages in this account
=> The same with my_second_email
Entry by default #mh/Mail/inbox [Button Explore]
Filtering configuration is here: /Configuration/Filtering
(In reply to comment #3)
> Sorry :
> Entry by default #mh/Mail/inbox [Button Explore]
You are saying that for both accounts, on the accounts' Receive page, you have set '#mh/Mail/inbox' as the 'Default inbox'? Unfiltered mail will land in this folder (Mail/inbox).
Yes I confirm. This enables me to have one folder to look at despite having two emails address.
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