Thank you lando242. Due to your response I got to believe there might be an issue with an extension. I have checked another computer with similar installation of Opera27 (but on win7) and it had same issue. So I reinstalled Opera and installed all extensions except SpeedDial FVD (google chrome extension). Et voila: I haven't had any issue yet with disappaering bookmarks. If issue reappears, I will report here...
Thanks for your help!