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):
http://ftp1.digi.com/support/documentation/ubootrecover.zip
These instructions include binary u-boot-cc9p9360js.bin which is U-Boot 1.1.6 DUB-RevF1
For NET+OS also check those notes:
http://ftp1.digi.com/support/documentation/importantinformation_for_the_connectcore9p9360.pdf
also check the knowledge base:
http://knowledge.digi.com/pkb_Home?q=U-Boot&l=en_US&c=Product_Category%3AConnectCore_9P_9360_9750%2CDevelopment_Environments%3ANET_OS
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/