Codeql-analysis.yml exists, but code scanning security tab disabled

TL;DR: How do I enable code scanning when codeql-analysis.yml already exists?

I recently had to delete a repository and re-fork it. After re-forking and enabling actions, codeql-analysis.yml runs, but immediately fails with “resource not accessible via integration” errors for CPP and Python. I believe this is because the repo security tab still says, “set up code scanning” and it is trying to write to paths that do not exist.

This has never been an issue in the past. I would just enable Actions and the rest was automatic.

If I setup code scanning, it wants to overwrite the existing codeql-analysis.yml configuration with a default config and I would have to create a new branch to avoid upstream conflicts.

Did I do something wrong when I re-forked? Is there a new procedure to follow? Nobody else I’ve talked to seems to have this issue.

Any assistance resolving would be greatly appreciated.