Thanks AmigoJack for opening a subject about locking "I have been hacked' topics".
I think it was a pity indeed, that my original topic got locked, as it could definitely help others to read the answers, I believe.
Before posting my topic, I tried to look for the best place to post it and noticed the warning on the support forum about not posting bug reports there. I went to the bug tracker report page. Got confused about how it worked, didn't understand why it couldn't be an open discussion on the forum, so I decided to post it publicly on the support forum instead, since I previously received great help there.
After Mick locked the subject and advised me to report it on the bug tracker, I did it. But I have to admit I wasn't too comfortable sending all the documents requested (the copy of the files and the copy of the database). I thought all the answers could probably be found from the log only.
I did receive an answer (thanks Noxwizard for taking the time to look into it), which confirmed which files had been added, corrupted, and in need to be replaced, but it didn't explain how it happen though.
I had already checked my ftp logs, and I knew it wasn't the protocol that had been used : it had only been used recently to access my server by me, when rectifying the issue. Only the http logs looked suspicious and were revealing.
AmigoJack contacted me by MP to explain it to me, just using the initial info posted : googling the code injected, he guessed that I had an other project hosted only server that could have been used as a back door to inject the malicious files and then access my board.
So his advice was really useful to help me remove the vulnerability I had on my server. The security breach wasn't linked to any phpbb bug in the end, but I wouldn't have known if I hadn't posted the issue publicly, and I would have left with the feeling it was...
In other words, I think it is essential to keep these topics open, to carry on sharing knowledge. And if a dangerous code or compromising code get posted, maybe the message could be edited to hide it ?