Due to various reasons, we had to update our kernel version number from 4.2.1 to 4.2.2. When we were using the 4.2.1 kernel version, we used the following dtb modifications in order to get USB to work on our custom carrier board: https://devtalk.nvidia.com/default/topic/1049988/jetson-tx2/third-usb-on-custom-board-not-working-with-jetpack-4-2/post/5330117/#5330117. Whenever we needed to, we were able to load xillybus into our kernel as a module with no issue and were able to easily interface with PCIe.
After upgrading to 4.2.2, we were able to use the same modifications to make USB functional on our custom carrier board. However, when it came time to load in xillybus as a module, we could not successfully load it into the kernel. My question is that in the above form, do any of the modifications (USB, UTMI, OTG) interact with any PCIe peripherals.