maikverge on "Odd Permalinks 404 error"

So, I did something stupid, I changed my permalinks to get rid of the /index.php before all of my page links, and now everything but my homepage is gone.

Even the new pages I create cannot be found.

I've checked the usual suspects. My .htaccess file is good

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

My rewrite module is active. I've shut everything down, rebooted the server, switched to default to custom and back and rebooted again to no avail.

I have a sneaking suspicion something in mysql database wasn't updated correctly, but have no idea what I'm looking for. If anybody has any ideas, I'm all ears.

Running a Debian 8 server with the most up to date versions of PHP/SQL/WP/Apache

Thanks guys.