The following is what I did to update all my bookmarks in Opera 9.5:
I'm on Windows XP. If you aren't using XP, you'll have to figure out the details concerning the operating system you're using.
Copy your existing Opera Bookmarks (.adr) file to a new file name just to be on the safe side. You can do that from within Opera (just right click on any bookmark for the menu) or from within Windows Explorer (file explorer, not Internet Explorer). My bookmarks aren't in the default location for reasons I won't go into here other than to say it's a convenience for me when I create system-backups. I don't even remember where Opera has them by default. I believe AM-DeadLink (discussed below) will automatically point you to that folder/directory. If not, it must be near the favicon image directory (old or new) though. Read on to see where to find that.
You can also backup your Bookmarks to a zip file using a menu item in AM-DeadLink, the free program you're going to use to update all your favicons in Opera 9.5+.
Download and install or update (doesn't have to be a clean install — just install right over the top of your existing program).
It's FREEWARE! "Free," doesn't that mean it's junk? They give this program away, because they know you'll like it and they have other programs that come in both free and enhanced versions for a charge. They also have a program you can't get for free at all. By the way, I'm not affiliated with them. I just use AM-DeadLink.
If you run into problems with the Beta, you can always reinstall the final 3.2. 3.2 though will not update Opera 9.5 bookmarks with favicons.
If you haven't used AM-DeadLink before, read the help section in the program. It isn't long. This will help you feel more comfortable and secure. The Beta version worked just fine for me. There is a progress bar at the bottom of the program. If you have a huge bookmark file (I do), be patient while AM-DeadLink loads your bookmarks into AM-DeadLink and while it checks your bookmarks.
When you go to check all the bookmarks in Opera, AM-DeadLink will ask you to inform it of the directory (folder in Microsoft-speak) where the favicons are stored. That folder changed locations from Opera version 9.2+ to 9.5+.
The old location was:
C:\Documents and Settings\[your user name]\Application Data\Opera\Opera\profile\images
You'll see your old favicons there.
The new location is:
C:\Documents and Settings\[your user name]\Local Settings\Application Data\Opera\Opera\profile\images
My user name happens to be Owner, because I'm the only user on my computer.
Now, go into AM-DeadLink's Options/Settings/Check and set things at the maximum settings: 30; 600; 3 and then plan to do something else while AM-Deadlink does the maximum job in checking your bookmarks. If you have a slow connection or older computer, you may want to drop that 30 down to 8 or even 4. At the very end of checking your bookmarks, it can take 10 minutes before it gives up on the last bookmarks. You can click "abort" if you get antsy at the end.
On the Bookmark tab, locate your Opera bookmarks file (.adr). On the FavIcon tab, select C:\Documents and Settings\[your user name]\Local Settings\Application Data\Opera\Opera\profile\images
AM-DeadLink 3.3 Beta-1 is still pointing to the old directory.
BE SURE you are under Documents and Settings\[your user name]\Local Settings and not Documents and Settings\[your user name]\Application Data; otherwise, you will have to move the AM-DeadLink output manually or re-run AM-DeadLink's check on all your bookmarks after re-pointing to the correct, new folder.
Okay, AM-DeadLink shows in the menu "FavIcons/Check Bookmarks and download FavIcons" and via a toolbar icon (Red Apple). Use either and be patient.
If it tells you that there might be a compatibility issue and you know you've selected the right FavIcon directory, click Yes.
If you have more than one bookmark file you check (as I do), select "Keep existing FavIcons." I say that just to be safe since this is a Beta version. I don't know for sure whether it would overwrite just the differences per bookmark or overwrite the entire file. I didn't test it. It probably just overwrites differences per bookmark.
When AM-DeadLink finishes checking all your bookmarks and favicons, you can save the file using the File/Save As on the menu. It will automatically create a back up of your bookmark file in the same directory. You can do lots of other things too, as you will see from the menu and by reading the help file.
You won't want to have necessarily deleted them. Think before you delete anything including even duplicates. It may be a long time since you create a duplicate in your bookmarks categories on purpose. I have lots of them. Also, a broken link doesn't mean you necessarily don't want to have the chance to go check the domain or root http directory. A dead bookmark might be the only reference you have to that website you may still want to have in your database.
Anyway, I hope this will help you. If it does, please let me know by leaving a comment to that effect.