Not sure if a solution is possible here.
The sqlite updater needs to run a query for pagelinks and its friends to find and fix the rows.

Thanks for the reply. I think I found the source of the confusion. I had been using Special:MathStatus to compare the output of the enabled math modes. But it appears that Special:MathStatus handles the mathjax mode differently from the rest of the wiki.

Thanks for the great information! I see now that it is more general than just $wgMathValidModes.

In T187883#8608549, @SacredSum wrote:

I also have this problem, with MediaWiki 1.39.1 and an SQLite database. PHP 7.4.33-1+deb11, Debian 11.6.

If I'm right in my guess about SQLite, this is a manifestation of T253199.

I have this too, with $wgProhibitedFileExtensions. It happened after upgrading from MediaWiki 1.39.10 to 1.39.11. It had not happened during any prior upgrade in the 1.39 series. I am using PHP 7.4.33.

I forgot that I had opened this task and almost went to open another one today. Anyway, a little more information: the problem still exists in 1.39.7. In addition to ignoring $wgUseImageMagick, the hardcoded getScalerType for webp also ignores $wgUseImageResize.

I also have this problem, with MediaWiki 1.39.1 and an SQLite database. PHP 7.4.33-1+deb11, Debian 11.6.

https://gerrit.wikimedia.org/r/c/mediawiki/core/+/803995/3/includes/media/BitmapHandler.php#404

// We only want to replace each of the variables once
$replacement = $matchLookupTable[$m[0]];
unset( $matchLookupTable[$m[0]] );
return $replacement;