I see the files named 'Bookmarks' and 'Bookmarks.bak,' but when I try to access from Opera by using "Import bookmarks and settings... > Bookmarks HTML file" the file is not shown as an option. Both files are not in folders and shown below all available folders when I search with file manager. I'm assuming neither are HTML files, and so are not shown as options.
You are correct. They're not HTML files. They're JSON files. You can look at them by opening them up in JSONedit in tree mode to see if your missing folder and bookmarks are there. In JSONedit after you load the file, right-click on "root", goto "expand", and choose "all" to easily see all entries.
Just for advanced info (that you don't need to do at the moment), if you wanted to convert that bookmarks file to an HTML file, you can do the following:
Create a test standalone installation in a folder named "Opera Test" on your desktop, and close that Opera. In the "Opera Test" folder on your desktop, there will be a "profile/data" folder. In it, will be a "Bookmarks" file. You can replace that bookmarks file with the bookmarks file from your regular Opera. Then, you can start the test Opera, goto the URL opera://bookmarks, and use the drop-down at the bottom left to export the bookmarks as an HTML file that you could then import into your regular Opera if you ever wanted to, and drag the missing folder (if it shows up) to where it use to be. Then, you can delete the rest of the imported bookmarks you don't need.