I'm on Olimex Lime2 with nand boot over SATA HDD with root mounted on it, and have the same problem over the last system update to 4.70:
sudo apt-get dist-upgrade
My system was on weezy with legacy kernel 3.4.109. Try to move to jessie with same kernel, following the procedure on documentation, but the problem remains the same with update:
Unpacking replacement linux-wheezy-root-cubietruck ...
dpkg: error processing /var/cache/apt/archives/linux-jessie-root-lime2_4.70_armhf.deb (--install):
unable to make backup link of `./boot/bin/lime.bin' before installing new version: Operation not permitted
Errors were encountered while processing:
/var/cache/apt/archives/linux-jessie-root-lime2_4.70_armhf.deb
Maybe is this a space or protection problem on nand ?