Had to wait for it to do a backup before I could show it.
It does this - I had previously removed the webcam device key, as well as ENABLE_MJPG_STREAMER, CAMERA_DEV, MJPG_STREAMER_INPUT, webcam, and snapshot. All I had was the printer USB port key - as you can see it's removed the printer USB port and replaced it with webcam device, which means the container doesn't start.
Now that I think about it - it could be because the printer is not powered on when it does a backup, so when it comes back the USB device does not exist, but I don't know why it would change the template.
I'll try creating an automation to turn the printer on during the backup window - however I have also tried setting community apps backup to ignore the octoprint folder, but it still happens. I've had plenty of containers where I've edited the templates and I've never had this happen.