I am not sure I understand. The process of restoring a complete XML backup (or cloning the entire Jira database) won't actually change the Server ID for that installation. The ServerID value is stored in the Jira database. So if you're migrating data via the system restore XML or via cloning the entire database, this value does not change on its own.
However there is a potential problem with having two applications on the same network with the same serverid. This serverID is used as a unique identifier in regards to creating application links between products. The act of cloning your current Jira install means that the clone can still behave as if it is the production Jira instance and still communicate with your other applink'd applications. This scenario can be problematic, and typically should be avoided when possible.
Could you explain further about what specific steps you are taking in order to migrate this data from production to a dev environment?
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