If you have set up application links to more than one of the same application type (for example, you have linked your application to two JIRA servers), then one of the servers will be the 'primary' link. This means that any outgoing requests will be directed to the primary link's application.
For example, if you have set up a Confluence server that is linked to two JIRA servers with two-way authentication for both links, you must specify one of the links to JIRA as the primary link. Every time Confluence requests JIRA information (e.g. for a JIRA issues macro), it will request it from the primary link's JIRA server. Both JIRA servers can still make requests of the Confluence server (e.g. a Confluence page gadget on the dashboards of each JIRA instance).
(This is true only for some linked applications; for example, if you connect JIRA to two FishEye instances, information about both instances will appear in JIRA, regardless of which application link is set as the primary link.)
Primary project links also control how information is shared between applications. See Creating links between projects.
To make a primary link, click the Make Primary link next to the application link that you want to make the primary link. The link is available only if you have set up application links to more than one of the same application type.