Solution
If you are unable to boot the X410 from eMMC, it is possible to boot the device into u-boot over JTAG. The will allow the filesystem to be reflashed from eMMC.
To do this, follow the process described in the Booting X4x0 over JTAG section of the X410 UHD Manual. This process requires you to use either the Xilinx SDK or the freely available Vivado Lab Edition.