I'm sure I posted this before my last post, but it wasn't approved. Or maybe I just didn't actually post it. If I did post it, please approve that instead of this.
AIUI, the OP received a 4TB replacement drive under warranty from Seagate, in advance of returning the faulty one. The OP then backed up the original data (plus some OS files from a 2TB drive) to the replacement drive. Now the original data are not visible to the OS, but the files are occupying the expected amount of space. Data recovery software can also see and access these files without error.
Yes, that is what happened. I used a warranty replacement to get a new drive of the same model that had been giving me issues, and also to take advantage of getting a fresh drive before the warranty ran out. I apologize for any confusion.
If DMDE only allows for 4k files at a time, that would be incredibly inefficient and not worth it at all. I have about 1.5 TB of data (mostly music). I have tried Recuva a bit, but I don't plan on using it because it does not preserve modification dates. That is key for me, and I'm so far not finding any free programs that have this feature. If anyone knows of any, let me know.
I'm not familiar with Ubuntu Live CD at all, and really don't know what that would entail. Not sure what ISTM means, but I initially suspected it was some kind of bizarre permissions issues, but others have suspected it's some kind of "corrupted directory"- what kind of corrupted directory and why, nobody seems to know.
@rogfanther, these are desktop drives. I don't know what you mean by "copy the data" and such, because I cannot access this data at all through normal means.