I’m seeing some conflicting documentation on this.
The install guide claims backing up or updating e-series robots requires an SD Card. Meanwhile, section 5 of the e-series maintenance manual suggests this can all be done with a USB.
We’re running polyscope 5.9, and the UI suggests USB upgrading/backing up is possible. However, I’d like to avoid bricking my robot if this UI is misleading.
Any insights?
The guide you’re linking (Install new image) is not related to updating the robot. As it says on the first page, it’s for installing a new image on the robot - in other words resetting the robot completely. 
When doing this you can take a backup from the SD card. They mention this since a reset often is performed if PolyScope can’t be accessed.
When updating the robot, you must follow the instructions in your second link. You can make a backup of everything by using the Support File button found on the Log tab.