Until its changed in your php settings, then nothing you do in Moodle can override those. They are the core settings for how your webserver works and Moodle is restricted to those settings BEFORE it can apply any of its own. Those php settings should not be the 5th place to check and to adjust, they need to be the 1st. As for your .htaccess working/not working or a custom php.ini in your public_html folder, again those are webserver issues to take up with your hosting provider.
They don't need to know Moodle (although it obviously helps) as, in the first instance, these are webserver php settings that are necessary before Moodle does anything, and Moodle can then only work within the webserver settings and does not (cannot) override those php.ini settings itself.
Get those core webserver settings sorted and THEN look at the settings within Moodle - site policies, course and assignment as required.
Unless changes were made to your webserver configuration at the same time as you upgraded Moodle, then your upgrade should not have had any impact on those php.ini values or your .htaccess file.
I can confirm that the server is set to 32Mb
Moodle is set to 5Mb
Course is set to 5Mb
But the assignment does not show the 5Mb option. Only 2Mb and below.
This is not a server issue now. There seems to be an issue between the assignment not seeing the course settings.
Check your assignment settings in the Admin/Plugins area. Perhaps it is locked there to 2MB.
I'm facing a conundrum where I have to update ~100 courses full of ~400 assignments that are all set to 2MB. Even though the maximum is set to 1Gb in all places, it is only some assignments that need updating but I don't have time to update it by hand.
Is there a SQL command to run to update all assignments? I was able to quickly find sql to update courses but unfortunately this does not affect assignments.....