Hi Omkar,
The easiest solution would be to use later images. They can be downloaded here: i.MX Software and Development Tools | NXP. Linux 4.14.98_2.0.0 and Linux 4.19.35_1.1.0 contain Linux binary demo files for i.MX 8M Mini EVK.
As for me, I really needed to use the 4.9.123 version, so like I mentioned above I disabled typec2_ptn5110 in the device tree (i.e., change status to "disabled" here: fsl-imx8mm-evk.dts\freescale\dts\boot\arm64\arch - linux-imx - i.MX Linux kernel) by applying a patch and created my own Linux image. Disabling the USB Power Delivery IC may disable essential features of the chip so please consider this a temporary workaround rather than a proper solution.
What sounds strange is the fact that your EVK previously worked fine with 4.9.123, which was not the case for me. This may mean that your problem is different and my suggestions may not apply to you, but I think it is still worth trying.