You can unlock files: https://central.owncloud.org/t/file-is-locked-how-to-unlock/985?u=tflidd
However, if it happens very often and you use the upload function a lot, you should install the redis cache for file-locking (https://doc.owncloud.org/server/9.0/admin_manual/configuration_server/caching_configuration.html#id4).
I don't use external storage where encryption provides a benefit. I would avoid shared folder or large folder that might not be completely indexed or are subject to a lot of changes.
Your webserver or php logfile, do they show errors? I mean if there are real timeouts, you should be able to find some hints. And you can monitor the server (CPU usage, ...). But you are on a 64-bit system?