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On Plesk for Linux mod_status is disabled on upgrades to improve Apache security. This is a one-time operation that occurs during an upgrade. You can manually enable mod_status later if needed.
I have those in the conf directory as well. Mine was breaking trying to load files that should have been in the vhosts directory inside of conf. Not sure why they weren't there.
looked for the saved config files that plesk saves when it upgrades and compare the current conf file with the old one.
previously I've had to restore older versions of my config files to get things working again. I would say that installs are MUCH better now than they were with plesk 6.. (totally manual back then).