Massive duplicates and the catelog

What exact version of Lightroom?

"I haven't (yet) found a way to tell Lightroom to rebuild the catelog with the images that remain in the folder. Please help."

After the duplicate finder program deletes the files that it believes to be duplicates, you should be left with one copy of each image on disk. Then, in Lightroom Classic, Library->Find All Missing Photos, and then you can remove all of these missing photos from Lightroom Classic.

I would make backups of everything (all photos and your catalog file) before you do this, just in case. DO NOT SKIP THIS STEP. See, this is a really really really really really really really really important step, that's why I told you in bold and capital letters not to skip this step. If you do skip this step, I will have no sympathy for you.

Once the images have been added to the catalog, they have been added. That record has been added to the catalog which is a database. I'm sure you are aware that the image itself is NOT the catalog. The catalog is just a database that keeps track of where the images are located on your computer as well as what adjustments you have made to those images and what collections you have added them to and other stuff. When you were adding these images, did you choose the option to not import suspected duplicates? Are you familiar with proper importing procedures? Are you familiar with using Lightroom Classic or are you a new user?

I am sorry but I really don't understand you question and your problem.

As I read your post I find several thing wrong with your method of cleaning and reorganizing your images.

First you should do all reorganizing of folders, Creating new ones and deleting, removing, old ones and Moving the images from one to the other Inside, With, LrC in the Library Module.

As for finding missing photos there is an option for that in LrC. Library module, Library menu item > Find All Missing Photos.

If you moved images outside of the LrC interface and then Reimported those moved images you have Effectively Lost all the edits you did on them.

I think 99% of the poroblems you are currently having, the reasons you find that you have to Reorganize your folder structure, is the lack knowledge of how LrC works and what LrC is.