Universal Missing files when syncing with iTunes

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I often transfer PDF files and videos from my Mac over to my iPad (or iPhone) using iTunes and a USB cable manually by dragging/dropping them into iTunes (this gives me the most flexibility as I'm not restricted to syncing only those PDFs I have in the Books app on my Mac etc.).

Once transferred I simply go to the Books app on the iPad, select PDFs from the library, choose to sort as Recent or Manually (they both appear to show the latest imports), press "Edit", then select all the newly imported PDFs and then finally "Add to.." and choose the Collection where I want them.
This works fine with a few files, but let's say I want to import 123 PDFs which I want to place in a specific Collection. I just tried that and ended up with something like 120 PDFs! So 3 are missing.
I can already see two problems:

1) (when having pressed "Edit" in order to select, and "Add to...") there's no way to tell how many PDFs I've already selected. All I can see on the upper right hand side is the total number of PDFs, but nothing about how many I've selected

2) I'm not sure if I'm really seeing all the recently imported PDFs. I've tried both "Recent" and "Manually" sorting, but nevertheless I'm getting the same result (missing files in my Collection)

If I go (in iTunes on my Mac, while the iPad is connected) I can click on "Books" on the left hand side of the window (under the "On my device" section and see all my PDFs, and by sorting them as "Date added", select multiple PDFs and see (at the bottom of the screen) how many I've selected. There are indeed 123 new ones to be found there.
How do you suggest I solve this problem and make the whole process easier?

 

[macstatic]

I discovered something interesting.....
Among the many PDFs I've tried to transfer, 3 of them are actually copies of the same file but with slightly different filenames. Still, only one of them can be seen in the iPad Books app.
Does iOS/iPadOS refuse file duplicates based on its content, or is some sort of ID created, unique to each PDF, so that if I duplicate it, this will confuse the Books app with (seemingly) the same file multiple times?

UPDATE: I think I've figured it out!
It appears I was right, guessing a specific file-ID is created, so that whenever a PDF file has been copied, and then transferred over to the iPad (both the original and copy/copies), only one of them will be available (the most recently transferred one as far as I remember).
The PDF in question was a PDF-save of a web page (File-Print-PDF-Save as PDF in Safari), so instead of creating a single PDF save then duplicating it in the MacOS Finder I repeated the process of saving the web page to PDF as many times as I needed, thus creating a unique file every time (despite the content being exactly the same).

I assume the same goes for duplicates of other file-types (i.e. MP3, JPG, MP4 etc) on the iPad as well.
Maybe someone more knowledgeable can shed a light on this, and also if there's a solution to transferring file-duplicates which can't be re-created like in my example above. In these cases, is there a way to modify some meta-data or something which makes a duplicate look different from the original?