Goto the URL opera://about and take note of the "profile" path.
Close down Opera and use Windows Explorer to goto the profile folder.
Delete the "History", "History Provider Cache", and "History-Journal" files.
Then, start Opera and see if deleting history via the UI works correctly. If not, you might have to goto the URL opera://settings/reset and reset your settings.
Do you Opera Sync?
Just Back up your current Profile folder and try to recover just the Bookmarks file (if has been backed up).
Right click on the file, Properties - Previous Versions.
Follow the Signature's Backup | Reset link to find the Profile and BKs file.
"Off Topic Tip"
Follow the Signature's Backup | Reset link.
Take the opportunity to start a Backup plan and even create a Template Profile.
SyncBack | Synkron helps.
Windows 7 (x64)
Opera Test profile | Back up | Reset