This happened several times in a row today. Each time I tried to update from 9.0.1->9.0.4 (by clicking the button in the admin module), nothing appeared to happen.
But, then MySQL crashed, as well as cPanel and a bunch of other Linux services. CRASH!
After restating the services and verifying all was stable, I waited a bit then clicked the owncloud "Update" button again. Same result. MySQL--> DOWN, as well as other services. And, my .htaccess file in another site had a "_" appended to it taking that site down, too.
Therefore, I did a virgin install of OwnCloud, but now I'm afraid the next time there will be an update to do. I can't spend an entire day installing owncloud, changing the database to MySQL, and all the other ancillary tasks, PLUS, restarting all the services on the server as users are calling me asking why their sites stopped working.
Hopefully, this Update issue was just a bug in the 9.0.1 release, but I wanted to mention it as it has taken about 7 hours of my day to get everything back up and running.
Look forward to any ideas on what might have happened.