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Yes, you can connect Align to multiple Jira instances, whether they be Server, Data Center or Cloud versions.
In this case, you need a separate Jira connector for each instance you want to synchronize with Align. You can combine data from the multiple instances into one single program or view them all separately. I worked with one client that had an Agile Release Train with the teams spread across 3 separate Jira instances, each with their own security restrictions.
We used 3 Jira connectors to bring the data into a consolidated view, shown below.
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