Just to state/clarify the obvious, the main purpose of using Bamboo's linked repositories rather than configuring one per plan/project is to separate repository changes from plans/projects that are consuming them:
Linked repositories are available globally to all plans and jobs configured on the Bamboo server. Doing this can save you from having to reconfigure the source repositories in multiple places if these ever change - any changes to a linked repository are applied to every plan or job that uses that repository.
Can you please clarify whether you actually need to change which linked repository is consumed rather than changing which repository the linked repository itself references (of course, you might e.g. want to change the repository only for a subset of consumers, but not others)?
Other than that, I'm not aware of a resp. REST API, unfortunately Bamboo does not expose its features via REST in a consistent way - speaking of which, there is also no REST API for linked repository configuration itself, please watch and vote for for the following improvement to increase Atlassian's priority to close this gap:
That being said, you might be able to achieve this via the Java API by means of the excellent ScriptRunner for Bamboo (BETA), which allows you to automate Bamboo via Groovy. You need to figure out the required code yourself though , i.e. I haven't yet tried to adjust the repository configuration via that route.
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