An unlocked bootloader is not the problem. If you somehow modified the system image ( like rooted/removed apps, integrated updates into ROM, installed custom recovery or something else) the update process will fail because of it. That might have to do with the fact its an incremental update which checks if it is modified/rooted and/or will update apps which aren´t there anymore.
One way to solve this is to backup your apps and data. Then flash stock recovery and stock image via fastboot and install all updates from the beginning.
The other way is to go to Nvidias Support Page for the Shield. Then download the latest Update for it. It´s an sh package which needs to be extracted under Ubuntu or special tool for windows. Then you can flash the newest image and recovery directly with fastboot. Didn´t try that.
Hope i was able to help you.