Macbook Pro w/ USB-C and multiple monitors occasionally swap non-main screens
So one "solution" is to unplug the USB-C cable from the computer and replug it in.  I have at times had to do this several times before it picks up the correct configuration. Its totally anecdotal but I have found better results by unplugging and plugging it back in immediately before the computer has a chance to reorganize the windows on the laptop. So its not like the information is somehow corrupt or lost, it must be triggered by the order in which it recognizes the monitors.