WordPress reading old version of functions.php, breaks site

The issue was indeed server side caching. Bluehost was very helpful in providing a way to fix it via FTP. Do the following:

In the /wp-content/mu-plugins directory, there is a file called endurance-browser-cache.php. By renaming the file, for example to endurance-browser-cache.old, visiting the site, and returning the name to endurance-browser-cache.php, WordPress will have had to force refresh the cache.

Good to know!