TimThumb not regenerating thumbnails

First of all, I know we shouldn’t be using TimThumb anymore but my theme has the script built into it and I don’t know workarounds to remove it without losing functionality.

The problem: Yesterday, I was testing out ways to harden WordPress as per codex instructions and so I added the following code to my .htaccess file:

# Block the include-only files.
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^wp-admin/includes/ - [F,L]
RewriteRule !^wp-includes/ - [S=3]
RewriteRule ^wp-includes/[^/]+\.php$ - [F,L]
RewriteRule ^wp-includes/js/tinymce/langs/.+\.php - [F,L]
RewriteRule ^wp-includes/theme-compat/ - [F,L]
</IfModule>

Perhaps unsurprisingly for most of you, this broke all the sliders etc that were using TimThumb to generate thumbnails.

I promptly removed
RewriteRule ^wp-includes/[^/]+\.php$ - [F,L]
from the file, but this still didn’t regenerate any thumbnails.

So I removed the entire code, deleted the cache, and waited–nothing. Then I confirmed whether the posts still have featured images (they do) so I figured, maybe it’ll take some time?

24 hours later, still nothing. What do I do?