I've only played with ecryptfs a bit, a while ago, but I tried to make sense of your story & failed.

It seems like there are multiple problems...
DanR wrote:My understanding
... and the user may not be telling you everything that's relevant ...
DanR wrote:is that the user copied the home directory folder to his backup drive (Formatted in NTFS). Windows displays the folders contents as 34GB
I assume here you mean the NTFS folder, and I also assume that 34GB is the expected size.
DanR wrote:whereas linux displays the directory as 200mb (ish)
I assume here you mean the ecryptfs filesystem (under its mountpoint directory). Or are you saying that this refers to the same NTFS backup directory as in your sentence above? Or do you mean something else?
What has the user done to his ecryptfs filesystem, which means he now needs the backup? Is the problem that he has deleted stuff from that filesystem by mistake, leaving only 200MB of files in it, when it should contain 34GB of files - is that what you're saying?
DanR wrote:I have tried to make a copy of the directory which i can work off
I assume here you mean the directory containing the NTFS backup, on the external (USB-attached?) disk, which Windows reports as 34GB in size.
DanR wrote:but windows only allows 15GB to be transfered.
And then what happens - I/O error? Something else? Is the disk itself healthy? Any errors logged at the relevant time in the Windows system event log?
With full & clear answers to those questions, there's a chance that I (or others) may be able to better understand the story and offer advice. Or perhaps I'm just being dumb today, and your original story makes perfect sense to other people