No, the bookmarks were lost as I said because I did restart of the system.
I've just tried to chown the whole folder and files of config/opera and now it works like with sudo, meaning bookmarks, sites logins, whatsapp, etc. are lost, but basic settings, history, etc. are now back again in normal mode.
I am just not sure if by default all of files of this folder are owned by normal user or some of them are roots one so that there is not any privacy leaks or sth.