When you program the FPGA portion of the SoC through the USB Blaster, the contents of the HPS SDRAM can corrupt the session. This noise might overwrite the operating system (OS) image in the SDRAM. In this case, the OS will not be able to boot up successfully.
Trigger HPS cold reset after programming the FPGA with the USB Blaster.
Alternatively, use boot software such as U-Boot to program the FPGA instead of using the USB Blaster.