AppLinks 3.5 Documentation
AppLinks 3.4 Documentation
No. You can add multiple instances of the same application (see More about Adding Applications) but you cannot use Application Links to connect two instances of the same application. For example, you cannot link one JIRA site to another JIRA site. You can link a JIRA site to a Confluence site, or a JIRA site to a FishEye/Crucible site, etc.