Have never approved of the "catalog" system used in any of Adobe's products that offer Organizers.
The Catalog file is not a container for your images. It is simply a file of "links" from the Organizer to the locations of images in your computer.
The Catalog system based Organizer in Elements is NOT interactive... meaning it does not watch and make changes based on manual changes you make in Windows Explorer. It does not survive data loss or file relocation resultant from a crash or meltdown. You must manually rebuild the system, or delete the catalog and rescan for a new catalog.
Once you lose the images and go to your backups and reload the images into to the computer, they are often in different locations than the "catalog" file in the Organizer originally found them.
I don't believe you can correct the Organizers Catalog file once a major relocation of images has taken place.
This corruption and breaking of links also occurs when you manual move image files and folders OUTSIDE of using the Organizer, as in simply moving files and folders in Windows Explorer and then going back to the Organizer... many broken links.
I have not used the Organizer in Adobe products for some time, so this info goes back a couple of years.
The solution is to be very certain that your images are in the computer in some order by viewing them in the Pictures/My Pictures system folder in Libraries. Be very sure this part is right.
Then, In Elements, there is a function for deleting the current catalog file. Then do an import and scan the computer Pictures folder to create a new catalog. You will drive yourself crazy if you try to use an old catalog or find an old catalog, based on the melt down of your catalog and system at use in the time.
Adobe builds this delete and rescan/import process into every version of Elements. It is common to have broken links and corrupted catalog files. They do not contain your images, but simply links to where the images reside in your computer.
The most important elements of your problem:
1) Understand where your images are actually located in the computer.. they are not in Elements, although they can be managed locationally by Elements Organizer.
2) Understand that once you start organizing using Elements downloader or folder view options, that if you go into your Windows Explorer and start manually moving files, you are going to break links locations in the Catalog in Organizer.
3) Pick one or the other:
a) Either manage files with the Organizer, or
b) Use only manual management in Windows Explorer, but
c) Never use both... one or the other.
Sounds like you must first make sure about the location of your replacement files from your backups using Windows Explorer and clean up any redundancy/other duplication.
Then you must deal with the catalog situation. Delete and rescan for a new catalog.
I first suggest you consider posing your question on the web site
www.elementsvillage.com, which is often looked over by techs from Adobe.
Adobe also has a very well run forum.
I would encourage you first ask this question on those forums. I would not consider UHH a good, responsive site to get answers for a question as technical as you pose. After all, aren't your images at risk?:
I have disable the Organizer in every version of Elements that I have used. I learned how to shut off the Organizer on ElementsVillage, and I don't use it. Neither do I support it's use by students unless they fully understand it's weakness and complexity.