To restore U-Boot boot loader you don't need Linux. There should be a U-Boot development toolchain included in the NET+OS for CC9P9360 CD/DVD.
On the Digi support page for ConnectCore 9P9360 http://www.digi.com/support/productdetail?pid=2801&type=documentation > section Documentation, you can find U-Boot recovery instructions (Windows Help file):
These instructions include binary u-boot-cc9p9360js.bin which is U-Boot 1.1.6 DUB-RevF1
For NET+OS also check those notes:
also check the knowledge base:
If you need a specific U-Boot revision which your firmware was tested with, get in contact with Digi Technical Support at: https://mydigi.secure.force.com/customers/