Does this organization-level secret still exist in GitHub?
Yes
Does the token still exist in SonarCloud?-
Yes
Does the user the token was generated for still have Execute Analysis permission on the repos?-
No. Looks this is root cause. Now May I know how do I regenerate new token which I can use for all repos. I do have full access right for GitHub and sonarcloud to fix this. But I am unsure steps to follow to create single token for all repos.
If the user no longer has Execute Analysis permissions, the easiest solution would be to grant that user such permissions again. No new token is required. Tokens are scoped to the user.