Damn, I feel so stupid now. As I was replacing the bookmark files on the stand-alone version, I realized that I had completely ignored one of the files I took as a backup, which was the BookmarksExtras-file. Copied and replaced Bookmarks file and the BookmarksExtras file and now it works. Thanks for guiding me into the right direction, even though probably this wasn't exactly what you had in mind

Damn, I feel so stupid now. As I was replacing the bookmark files on the stand-alone version, I realized that I had completely ignored one of the files I took as a backup, which was the BookmarksExtras-file. Copied and replaced Bookmarks file and the BookmarksExtras file and now it works. Thanks for guiding me into the right direction, even though probably this wasn't exactly what you had in mind

I'm trying to check if there is something wrong with Opera's profile or maybe with the bookmarks file.

I'll try it out tomorrow and report back to you. Unfortunately today is a busy day.

That's strange.
If you do a clean standalone installation and replace its bookmarks file with yours, what happens?

I don't know what difference it would make as I already took the bookmark files on my USB memory stick (from the previous install), formatted my HDD, installed a whole new version of Windows, downloaded Opera from the internet, installed it on my computer and replaced the bookmark files with the old ones.

Not even on the folders at the left?

Nothing there. That's the first place I checked.

Is there an "Imported bookmarks" folder in the tree to the left of the Bookmarks Manager?

Nope.

Also look under "My folders".

Nothing there.

Click on the heart icon on the navigation bar at the left of the start page or go to menu > bookmarks > show all bookmarks.

Nothing there.

If you open the bookmarks file in a text editor, do you see references to your bookmarks?

Yes. That's what I meant by "doing it manually one by one", which I'd very much like to avoid as there are so huge amount of bookmarks

Yes. That's exactly what happens.

Do you see anything in the bookmarks manager?

I'm not sure what you mean by bookmark manager exactly. As far as I know, I've checked every possible thing that is somehow related to bookmarks in the Opera settings (and with Import & Export addon). And while I can import the file as .html and then export it, it still doesn't help.

What happens when you replace the Bookmarks file? You don't see any bookmarks?

Yes. That's exactly what happens.

Hmmm, now that you mentioned it. I did save the original file also (didn't realize until now that .bak is a backup file). It doesn't matter though, as I already tried replacing the new with the old one and it doesn't help. No idea why.

So, I messed up. I just changed my OS from 32bit Win7 to 64bit Win10 today and I forgot about the option to export the bookmarks file and I just grabbed it manually from the folder to my USB memory stick. Turns out that it doesn't work when I use copy and replace.

Any way to restore the huge amount of bookmarks other than to open the file with notepad and do it all manually, one by one?

The version of Opera on Win7 was 41.0.2353.56 and it's the same now.