I ran a test update on a client’s WordPress website using our test environment and was surprised to see that updating to WordPress 3.8.1 killed all permalinks. Not good. The website used WooCommerce and after some investigation I managed to find a work-around: completely delete WooCommerce and re-install it. This will require you to reconfigure WooCommerce in the back-end Administration. None of my products appeared to have been touched so that’s a plus.
As of writing, WooCommerce is officially compatible with WordPress up to 3.7.1 with 4 people saying the plugin is broken in 3.8.1. That ought to be sufficient warning but the support forum only has a couple complaints. One thread even identified the issue as a conflict with Yoast SEO.
I figure there must have been some conflict with the page routing because not only were WooCommerce pages throwing a 404 but ordinary WordPress pages were as well. When I fell back on WordPress’ default hyperlink structure, everything was hunky-dory. Since Yoast SEO also has options affecting permalink structure, I wouldn’t be surprised if this and plugins like it would further complicate the issue.
If your WordPress website is using permalinks and you find that updating to 3.8.1 causes pages to throw 404 errors, I hope this helps you.