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To authenticate, go to your user profile or some dashboard with the Activity Stream gadget and click Authenticate with <...>

Corner case:

Sometimes , that authorization window is not present at all and you may need to whitelist the Jira instances.

  1. Go to Systems - Security - Whitelist
  2. Add a new record in the whitelist table with the following values
    1. Expression = domain of the other Jira in the following format "https://{domain}/*"(don't forget the /* at the end)
    2. Type = Wildcard expression
    3. Allow incoming = true
  3. Repeat steps 1) and 2) on a second instance
  4. Recreate application links

    Now, in both Activity streams you can see authentication windows.
    Keep in mind, that its necessary to authorize the connector in both instances (both activity streams).