After the update, I noticed that several images (including /resources/assets/logo.png) are missing. I think it's possible (for the logo at least) that they were deleted during the update. I don't know why that would have happened, and I can't seem to find any trace of them anywhere.
I fixed it. Avatars key need to be reuploaded though. I had to reclone the git repo because of conflicts. When I moved the images folder back to the document root, I forgot to delete the already existent images folder resulting in the images being in /var/www/html/images/images