I have created Board #2 in my project, and I can filter issues to populate the backlog for Board #2. How do I create separate sprints for Board #2 that do not replicate in Board #1?
Sprints are assigned to Issues, not Boards. Any Issue that is in a Sprint will cause that Sprint to be added to all Boards that the Issue is part of. The converse to this is that you cannot have an Issue that is in more that one Sprint.
I think that answers your question. If not, please provide more details on what you are trying to do and we should be able to help.
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