My webserver is crashed after 11.0.9 Update #56 auto update

[mavera2]

Regularly I get Plesk auto update mails. Yesterday I get this email.

Attention,

Parallels Panel was successfully updated.
To view the list of changes, visit http://download1.parallels.com/Ples...htm?platform=unix&locale=en-US&version=11.0.9.

This message was sent automatically by Parallels Installer.

I get this email in 03:29 local time. And I found I out that all my website crashed.
* First I get directory permission errors, My codes needs to write inside some folders but it couldn't due to lack of permission. But until that time it had permission. I changed permissions with chmod and it started to work again. But earlier I suppose it had 644 permission. Now I made it 777 to be usable. But I'm not happy with it. It didn't work with 644.
* After system working, I get huge swaps. It started with 5 MB and became 1300 MB swap file. After some time my MySQL server crashed and I rebooted my machine.
* As I don't remember wrong, I was using PHP as FastCGI, but when I check Plesk now, I see that PHP is run as Apache module.
* Does auto update changed these preferences ? I don't remember it was happened before this auto update.

I need to restore my server settings back. But I don't know what had changed since then.
How can I found out all changes to revert back ?
Thank you in advance.