Had the very same problem with Opera Windows version.
Please check "Imported Bookmarks" in Opera 25 and check all folders. I cannot remember the exact name but is was something like root_usr or usr_root. Just drag-and-drop them into new bookmars.
Otherwise check folder "%APPDATA%\Opera Software\Opera Stable" - there is a file called "Bookmarks" (with no extension). You can open it with any text file viewer and extract your old bookmarks manually.