You can not restore directory from user root and group root too.
With onyx you can not guarantee application security you have not full backup and restore of domain.
Plesk Onyx can not make property restore. This is the bug in software and cause is not the migration.
We have set a new domain and new web application and restore don't work property.
Wellcome to club:
after plesk team "have repair my server" i can not resore database too.
Failed deployment of database ....
Failed to restore the remote database ..............It cannot be restored for security reasons. Please contact your hosting provider to solve this issue.:(
But this is not just problem of migrate from plesk 12.5 to Onyx.
I have set new domain and install for probe new appolication (joomla).
Have make backup and at restore is the same problem only separate restore works.
Have solved it with wery primitive solution. Restore partial "Website" and system dont show "Command options error: "-ip" option is required for "-hosting" option" and backup are ok.
You can restore data of domain and database separate and it works good too.