Ok, I've succeed with the migration by following these following steps.
1. Dump using mysql-dump of my old LimeSurvey v3 instance
2. Import using mysql CLI command on my new LimeSurvey v6 MySQL db.
3. Run `sudo php -d memory_limit=-1 application/commands/console.php updatedb` on the command line.
4. After a while, I got the error mentioned in my first post. I don't "care" and rerun the exact same command.
The difference is that, first, the update message was `from 359 to 612` and, the now `from 418 to 612`.
As stated by you Denis, so, there is something "wrong" with the Update_419 script. That script is creating two tables: 
    github.com/LimeSurvey/LimeSurvey/blob/ma...es/Update_419.php#L9
 and 
    github.com/LimeSurvey/LimeSurvey/blob/ma...s/Update_419.php#L23
5. In open a MySQL console and drop these two tables using `DROP TABLE myprefix_xxx;`
6. I rerun the  `sudo php -d memory_limit=-1 application/commands/console.php updatedb`  for the third time and it'll fail again.
7. I rerun for the fourth time  `sudo php -d memory_limit=-1 application/commands/console.php updatedb`  and now, the message is `from 420 to 612` so, now, I've to check the `Update_421` script. Identify there tables; go to my MySQL console, drop the table and continue...
In my situation, I had problems with 419, 420, 446 and 480.
I've absolutely no idea why there is a `createtable` function in the php scripts for tables already present in my LS v3.x database.  These tables were present by empty.
So, for me, the issue is solved. I'll copy this message in the bug (
    bugs.limesurvey.org/view.php?id=19385
)
**Merci pour ton aide Denis.**