I was playing around with different plugins:
w3 total cache
jetpack - photon
With w3 total cache - I minified files manually
Emptied/purged the cache
Broke my homepage
Uninstalled all plugins
Homepage was broken
Did a temporary fix and moved in my homepage php file.
Is it possible that a plugin or the act of minifying files will actually change my PHP files?
Now my hover navigation buttons are not showing up. I don't know if it is a problem with my PHP files or CSS files (I don't know how or why any of these would have changed).
Any insight would be greatly appreciated.