I'm building a system, which needs GPIO access on a x86 machine.
The GPIO access works great. However, it falls apart once reboots come into play:

Plugging the PIZero in, lsusb shows Broadcom Corp.
If rpiboot loaded the OS on the PiZero and the PI is connected to an USB port that remains powered after shutdown, a reboot does not break anything. You can still use pigs for instance, after the x86 raspbian booted.
However, if power is cut or if the Pi is connected without loading the OS via RPIboot prior, then the linux kernel fails to boot properly and throws
device descriptor read/64, error -110
a couple of times with the last error being
device not accepting address 4
and all devices on that USB controller are blocked until the RPI is removed (Mouse / Keyboard are not active on Raspbian desktop).
It does not show up in lsusb and obviously rpiboot fails to find anything. Unplugging and plugging the usb back in solves this beheviour.
If it is still connected and a shutdown is initiated in that state, then the shutdown does not finish and remains stuck until the RPi is disconnected, with the same errors being thrown.

This issue may be a firmware bug and may be related to this issue with similar symptoms: raspberrypi/linux#2684

I want to make an automated system, currently physical interaction is required if the system is unplugged from the wall.
Leaving a Post-it on the machine saying "please unplug und plug back in that USB cord in case the system is moved or unplugged" is not an option ;]

Is it possible to update to a more recent kernel like the Linux 4.14 kernel available at https://github.com/raspberrypi/linux/tree/rpi-4.14.y (via https://www.raspberrypi.org/forums/viewtopic.php?f=29&t=197689)?

Would it be enough to change this line https://github.com/raspberrypi/gpioexpander/blob/master/gpioexpand/configs/gpioexpand_defconfig#L13 or are there more changes needed?

I was just going through the process of compiling this (trying under Ubuntu in Win10 among others)
It needs python, this at some points needs moving to use python3 so I don't have to install python (I have python3)

I just attached my new 3A+ with usb male to male cable to Pi3B+ (with no microsd card and no extra power). I see the popup in raspbian, select gpio expander choice. Then it uploads kernel and gpioexpander rootfs however then the progress bar stops before final step and nothing happens.

I suppose the build (kernel, rootfs) is simply old and does not support pi 3A+ yet?

BTW there was another issue that it didn't work at all previously due to conflict with usb host boot, see https://www.raspberrypi.org/forums/viewtopic.php?f=63&t=227044 however this is not the issue. I clearly see my new PI 3A+ is trying to do usb device boot and I see the popup with rootfs choice and broadcom usb boot device in kernel log on pi3B+.