You can switch between them, but the device tree (and perhaps other software) will have to change with it. Each manufacturer provides their own “board support package” (BSP), which is placed on top of the flash software. Perhaps there is a different kernel as well, don’t know, but it would be rare for there to not be a different device tree.
As far as “best practices” go, you would want to clone the rootfs (if it has value to you) before you do anything. A copy of the clone could be used in different ways to make sure that the next flash contains both the new BSP and the old clone.
In all cases where a clone is involved you would want to make sure the same L4T/JetPack/SDK Manager release which produced the original install is used to produce any updates.
If you know the content of the BSP from both carrier boards, then it might be possible to predict if a partial flash of just a device tree would work, but even if it does, it would be unsafe to not have a clone ready (if you value the existing rootfs).