Ultra - 96v2 board hardware manager Issue

I’m using ultra - 96v2 board for my project. I’m booting the SOC with micro SD card ( using boot.bin and image.ub). It works good.

but If i connect the board with Vivado 2018.3 hardware manager through Xilinx JTAG cable, it stops the functionality of the FPGA.

Also it stops the booting of SOC from the SD card, when i connect with hardware manager.

What is the reason for this issue? What are the things need to change to solve this issue.