Below are the two methods,
Method 1: The eMMC can also be programmed by following the Linux User manual, but only with Vitis 2019.2 or other versions (except V2020.1). Because, 2020.1 version has a known issue in JTAG programming. So, another version of Vitis tool can be installed and checked.
Method 2: The other method to program the eMMC is with Vivado tool and the procedure is attached.
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Please find the detailed product information here:
Zynq™ UltraScale+™ ZU19/ZU17/ZU11 MPSoC System on Module