I would like to check quite interesting situation that we are facing now.
I already asked the question about the Bamboo licenses limitation and seems there are no solution yet - https://answers.atlassian.com/questions/323522/bamboo-remote-agent-limit-100
So now we are going to install the second instance.
Now I have a questions:
1. Is it possible to set up the Application Link between the two Bamboo Instances? If so are there any complication if the Project Keys and Plan Keys will be the same?
2. What will happen if I link 2 Bamboo instances to the one central Jira? Again any complications if the servers will have same Project Keys and Plan Keys?
I think you should be able to set up a link between two Bamboo instances (it's a generic feature), but it won't be used for anything.
Bamboo supports linking with multiple JIRAs and JIRA supports linking with multiple Bamboos. You can have per JIRA-project default servers.
In general case, when dealing with key clashes, JIRA will go through Bamboo servers in the order of priority (you can make one Bamboo link a primary link). It's recommended not to mix the keys though, and it's enough to ensure that Project keys don't clash, plan keys can be the same across different instances.
Off topic a bit in your case, but Bamboo, when dealing with multiple JIRAs also supports per-project prioritisation of a link, you can assign JIRA projects directly to a Bamboo project.
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