After some more reading and some help from other members here I managed to sort it out, even with my limited linux skills.
I found the sh script on the mybook that performs the factory reset, after some reading I figured out that it uses a partition file ./etc/DSKPART to repartition the drive when resetting it. with the original DSKPART file the partition it created on the 2TB drive were invalid resulting in some strange issues.
The Original Contents of the file was
When I did a Factory reset i Got a disk with 927GB of space on /dev/sda4, but sfdisk -l display a partition that looked like this.
Device Boot Start End #cyls #blocks Id System
/dev/sda1 4 247 244 1959930 fd Linux RAID (autodetect)
/dev/sda2 248 279 32 257040 fd Linux RAID (autodetect)
/dev/sda3 280 402 123 987997+ fd Linux RAID (autodetect)
/dev/sda4 403 18574595212114498547 185745952121145142548 9276584568
fd Linux RAID (autodetect)
I then Changed the DSKPART File to
And ran the factory reset again and it worked.
Whithout that change the factory reset did not correctly partition the disk.