That sounds bad. The pref related to this is called "site_layout" and the default value for it is "basic" - deleting that row if present will revert it to the default.
You'll probably then have to clear all the caches afterwards which you can do from the command line using:
php console.php cache:clear --all
Mind you, those layout files live in templates/layouts as you found, so i'm not sure why it's not checking in there at all, no matter what the site_layout is set to... maybe there is a fault in 14.0 for your particular case, so perhaps try one of the recent daily tarball builds? We're close to releasing 14.1 so maybe something was fixed in the mean time?
Hope that helps, maybe join us on IRC for some more interactive help?