Not all iTunes Files not showing up on External HDD

My old TC (the flat model from back to 2008 I think it was) broke down the other night so I removed the WD 2.0TB HDD (containing over 30'000 music files) to run this as an external HDD. I had swapped the original 500Gb with a 2TB drive which worked super for a couple of years.
Anyway, before all of this happened all songs showed up on iTunes and each single one could be played correctly from iTunes (without the ! should the file not be found) so all files were located through iTunes to the correct directory. Only one directory for my Music files...
Now, when I connect the HDD through an USB cradle (nothing has been touched on the drive) only a fraction of the files actually show up in the directory which is very odd indeed? I believe it was the same when the thing was actually working but didn't give it a think as it was doing what it was expected to do.
Next step was that I copied the whole HDD over onto my MAC and sizewise all (?) the files came over but still not all are showing...
So, how can I make sure all the files are being included as I want to move them all over to my new 2TB TC?

Thanks Limnos for taking your time with this.
Here's what happened
1) All my Music was stored on a TC 2.0TB WD hard disk which I shared with my partner.
2) All music in iTunes were mapped to this specific location and only this location.
3) When opening the folder on the TC only a fraction of the actual music folders were available to see (i.e. Artist The Wonder Stuff folder was present and in this folder only 2 album folders were found when in fact there should have been 12)
4) All songs in iTunes did play correctly so if i wanted to listen to one of the The Wonder Stuff songs they would all play (even albums that did not show up in the artist folder from above).
5) When clicking show file in finder, the file would show up and then again when going back manually into the folder as above.
6) TC dies on me. No more power.
7) Took out the HDD and put it in a cradle to extract the songs.
8) Right click on the folder shows there are about 35'000 files which sounds right BUT only a fraction of these can be seen.
9) Now I cannot do the show in finder through iTunes as the directory no longer exists (the TC died and I threw it away, except for the HDD).
10) The files are on the HDD but I cannot see but a fraction of them when opening the folder...
I hope this makes it a little more clear.
I honesty do not know what to do as I know the files are there but cannot see them and thus map them in iTunes... :-(

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