hi, thanks for the suggestion. I think I treid it already, but I just run it again and I can see the same error. The full repair log:
Reconfiguring the Plesk installation
Started bootstrapper repair procedure. This may take a while.
Certain actions may be skipped if not applicable.
-- Warning: Skipping the data of table mysql.event. Specify the --events option explicitly.
Finishing up upgrade procedures and rerunning previously failed upgrade actions...
===> Cumulative APS controller database (apsc) upgrade and repair has been started.
===> Cumulative upgrade and repair of APS controller database has been completed.
===> Cumulative APS controller upgrade and repair (final stage) has been started.
===> Cumulative upgrade and repair of APS controller (final stage) has been completed.
===> Cumulative Plesk database upgrade and repair (revertable stage) has been started.
===> Preparing Plesk database upgrade (revertable stage).
===> Cumulative upgrade and repair of Plesk database (revertable stage) has been completed.
===> Plesk database scheme upgrade has been started.
Applying migrations from: /usr/local/psa/bootstrapper/pp12.5.30-bootstrapper/migrations/
===> Plesk database scheme upgrade has been completed.
===> Cumulative Plesk upgrade and repair (final stage) has been started.
===> Preparing Plesk upgrade (final stage).
===> Cumulative upgrade and repair of Plesk (final stage) has been completed.
WARNING: key file (/etc/rndc.key) exists, but using default configuration file (/etc/rndc.conf)
WARNING: key file (/etc/rndc.key) exists, but using default configuration file (/etc/rndc.conf)
rndc: connect failed: 127.0.0.1#953: connection refused
Reconfiguring mail subsystem...
Reconfiguring Apache web server...
/usr/lib64/plesk-9.0/services/webserver.apache: line 466: $config.new: ambiguous redirect
cat: write error: Broken pipe
mv: target `/etc/httpd/conf/httpd.conf' is not a directory
/usr/lib64/plesk-9.0/services/webserver.apache: line 466: $config.new: ambiguous redirect
cat: write error: Broken pipe
mv: target `/etc/httpd/conf/httpd.conf' is not a directory
/usr/lib64/plesk-9.0/services/webserver.apache: line 466: $config.new: ambiguous redirect
cat: write error: Broken pipe
mv: target `/etc/httpd/conf/httpd.conf' is not a directory
[Tue Jul 05 10:53:18 2016] [warn] module security2_module is already loaded, skipping
[Tue Jul 05 10:53:18 2016] [warn] module unique_id_module is already loaded, skipping
Reconfiguring ProFTPD FTP server...
Reconfiguring AWStats web statistics...
Reconfiguring WatchDog...
Restoring SELinux contexts...
Reconfiguring SSL ciphers and protocols...
Regenerating web servers' configuration files...
Cleaning active Panel sessions...
Bootstrapper repair finished.