Upgrade from 4.3.1 to 4.6.9 (Joomla) = fails; DB upgrade freezes
Are you upgrading directly from 4.3.1 to 4.6.9? 

If not, it might be worth trying a more incremental upgrade (e.g. 4.3.1 to 4.3.7, then 4.3.7 to 4.3.8 in case there's a sticking point there, then 4.3.8 to 4.3.11, 4.3.11 to 4.4, and so on - it's tedious, but may stop the upgrade from stalling, or give you an error message you can follow up.