I’ve seen this issue a few times on the forum, and I’m not sure what I can do to correct things. I’ve allowed .htaccess overrides in my virtual host, I’ve tried the .htaccess-bak method, I’ve destroyed and re-created the server while re-installing LAMP and WP. The ONLY pages that do not work when permalinks are changed are the Pro-related links in the sidebar that allow theme customization. Setting permalinks to default works fine, but isn’t an acceptable approach.
It looks like this issue is happening with multiple themes, so this is some kind of configuration issue. I’ll need to take another look.
OK, I did some troubleshooting. I’m not sure how relevant this issue is, but I’ll post the solution in case someone else runs into the problem.
This only applies to those hosting their own apps on their own server (linode, digital ocean, etc). For Digital Ocean, there is an SSL walkthrough to secure your website. During that process, a new sites-enabled configuration is created for your website. When this happens, the bot excludes the AllowOverride All directive which causes the links to 404 on SSL-secured sites. Make sure to include this! 
Hi,
Sorry for the delay and thank you for sharing your solution.
Cheers!
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