Catalogs and the Backups Folder
The main concept you need to understand here is what a Lightroom catalog is. It's not all your image files in one big file. The Lightroom catalog is simply a database that Lightroom uses to tie together all the information about your images. Where the original image file lives, the edit history of each image, tagging, collections, sets, etc. This is all in the
.lrcat file we call the catalog. Lightroom, by default, creates this catalog in the Lightroom folder with all your images. But you can put it wherever you want, and you can have multiple catalog files if you wish.
Whenever Lightroom backs up your catalog, it's making a backup copy of your .lrcat file, and compressing it with zip. You may also want to know that the .lrcat file is simply a SQLite database file.
Why you have ?s
In the database, each image has a path to where the original image file is on your system. If you move/add/delete files outside of the Lightroom application, as in using your operating system's file system, like when you did your "backup" to an external drive, the database will have a broken link in it, because that path is no longer up-to-date. If you plan on doing a massive file move, it's better to do it by dragging and dropping in the Library module of Lightroom. This will work for moving all your photos to an external drive, if you want.
Fixing the Issue
However. The only thing that's wrong with the catalog is that the paths for the files are out of date. All the other data--so long as you haven't edited or messed with the catalog, such as deleting the ?'d images--is still intact. All you have to do is fix the path. You can do this in two ways.
If you want things back the way they were, then simply close Lightroom, and copy the backup Lightroom folder back to where it was on your internal drive, so your external drive copy is actually a backup, and not a move. Then, when you open your original Lightroom catalog, everything should be back the way it was.
If, however, what you wanted to do was move all your images to the external drive, permanently, and you'd like to update your catalog to use the new path to the external drives, and so long as you haven't moved things inside the Lightroom folder itself, then you can simply update the paths:
Go to the Library module in Lightroom.
Right-click on the top-level of the folder where you keep all your Lightroom images.
Select Update Folder Location...
Navigate to the external drive, and select where the folder really is.
The ?s should now be gone.