Hey,
i think this could be caused by a current known and documented issue in 10.12.0:
If you have installed ownCloud 10.12.0 in the combination of:
index.php-less setup
URL via subfolder
the files view in the web UI will be empty. The desktop app will not be able to sync and an error 405 (Method not allowed) will be thrown. A fix is in progress and will be provided asap. Note that owncloud Server 10.11.0 and earlier are not affected.
Workaround: until the fix is provided, use the
.htaccess
from your 10.11 backup in your production system.