I've had reports of this happening on a system upgrade, or sometimes when a course is copied. I've not heard of a means to keep this from occurring but can tell you one thing to always check. Check that LTI is enabled at the course level.
I've often had questions like "Where do I find the Q4 2018 Learn Installer?" This brief video shows you how to use Behind the Blackboard to find the installation package you are looking for.