RESOLUTION
In case of default permissions on domain folder are lost; the following actions can be performed to restore them:
In Plesk panel go to Domains page, mark required domains and click on Check permissions button. Then uncheck Check-only mode checkbox and click OK.
If it is necessary to repair permissions for all domains, you can launch Plesk Reconfigurator ( Start, Programs, SWsoft , Plesk, Plesk Reconfigurator ), when it is run, choose Repair Plesk installation , then toggle on Plesk virtual hosts security and click on Check button.
Note: Please be aware that any custom permissions which might be configured by customers will be replaced with default ones after this action.