I know this is a bit late..but here's my workflow that I'm working on to mitigate this issue:
1. Unpack the cartridge in a sample course.
2. Move (using the course copy API (for now)) the cartridge to the courses that would use the cartridge.
3. Use the API to find the external tool that cartridge creates and edit the LTI key and secret.
In effect, I'm doing this manually...but automating my manual workflow via the API so that I'm not doing it so many times. In my test cases, it seems to have worked...we'll test on a larger group soon. (BTW--I'm using Postman to do this, as I'm not a big coder)...hope this is helpful to anyone who may have this issue.
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