Upgrading from 4.1.5 database to 4.6.2 failing with constraint violation
I recommend you take smaller steps, starting with 4.2. You can download the latest version of 4.2 from sourceforge (the latest in that series is currently 4.2.20).

If that upgrade goes ok, then you could proceed to 4.4 (the current LTS) and then up to 4.6.

Remember to backup your database before upgrading, and if the upgrade fails, restore from the backup before trying again.