Githib might restrict number of OAuth access tokens for a Jira DVCS connector set up with one account
Currently a DVCS connector is setup with a authorizing service account and OAuth id/secret to link with github organization based on linking-github-repository-with-jira.
The service account might have access to a number of organizations. At times users might link a new account for a new organization using the same id/secret combination used for the service account, resulting in one oauth app for multiple organizations. This resulted in JIRA at times running out of a number of access tokens allowed per user/application/scope combination. This is documented under https://developer.github.com/apps/building-oauth-apps/authorizing-oauth-apps/
Collect any supporting logs from github to identify any possible problems with authorization or generation of a access token. In the current scenario, the github logs show errors similar to below
oauth_access.destroy OAuth application (JIRA GitHub DVCS) deleted automatically (max accesses for application) Performed by xxxxxx from (United States)
It is suggested to create a unique oauth app for each organization in github to avoid running into a similar issue.