Thanks for checking out the ILI9341 display library! It sounds like something might be changing the device tree and removing the SPI device perhaps. When you see that error occur, can you run a command like this to check if there are any SPI devices available?
There should be a couple devices listed, like /dev/spidev1.0, /dev/spidev1.1. If you don't see any spidev devices listed then that does seem to be the issue, that something is changing the device tree to remove the SPI device.
One thing to try to force the SPI overlay to always be loaded at boot is to edit your boot config to load the overlay. Check out the instructions at the very end of this page:
https://learn.adafruit.com/user-space-s ... 2-8/wiring You'll want to connect to the BBB and run these commands to make the boot config editable:
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mkdir /mnt/boot
mount /dev/mmcblk0p1 /mnt/boot
Then use the nano text editor to open the config and add a new line at the bottom with the device tree overlay config:
The line to add to the file is this one:
Then save the file (Ctrl-O) and quit (Ctrl-X) and reboot the Beaglebone Black. Let's see if forcing the SPI device tree overlay helps keep it stable, thanks!