Updating WP destroys site

The other day updated WP and it crashed the site. Today I restored a backup and defender suggest again (this is what lead to the crash):

"REVIEW CHANGES

It seems the /wp-includes/version.php file is currently using by another process or isn't writeable.
FILE COMPARISON
Not Found
AUTOMATE RESOLVE
This will overwrite the file /wp-includes/version.php with the official WordPress /wp-includes/version.php file.
DOWNLOAD AND PATCH"

When I download and patch I am prompted to update Wordpress:
"WordPress 4.5.3 is available! Please update now."

Last time I updated, it crashed the site. It removed all of the pages and menus from the database.

I am not sure what to do.