4.1 Database Upgrade problem..

Best I can give is to do a manual update, if it gives and error this will help us fix it. (When the auto update gives an error to the effect that “Something unexpected happened”, I find it quite unhelpful.)

Details here:
https://codex.www.ads-software.com/Upgrading_WordPress_-_Extended_Instructions

Just tried that.
However, as soon as I try and run the upgrade, it (eventually) generates a 500 error. I still can’t get into my admin area. ??

I solved it. I got the database version from the options table and inserted it into the “version.php” file in wp-includes.
Shazam!

I suspect that you are cheating here.
Can only hope that you don’t get punished.
The question is, “Has you database been updated ?”, have the tables been adjusted ? It turns out that there are no new fields, no changed fields, but there is an index that needs to be removed by this code:

if ( $wp_current_db_version < 30133 ) {
		// dbDelta() can recreate but can't drop the index.
		$wpdb->query( "ALTER TABLE $wpdb->terms DROP INDEX slug" );
	}

Check for this in your phpmyadmin, delete this index if it is there.

Does this upgrade issue affect upgrades from version 4.0 to version 4.1?
I’ve already checked the options table and the mysql version is 5.0 in the table as well as in wp-includes/version.php

Any advice is welcome!

Does this upgrade issue affect upgrades from version 4.0 to version 4.1?

Yes, in version 4.1 (and beyond) the index called “slug” on the terms table is to be removed. A change in 4.1 requires that the index will no longer be unique (the ambiguities created are resolved), but you don’t want the database getting confused about this.

I am placing our community on notice that the presence of this index post v4.1 will be a source of taxonomy errors.

The mysql version is not relevant in this context, we are talking about the tables, fields, indexes etc as used by WordPress.