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Editing Java Specs for plans with active PRs requires deletion of PR branches

I have around 50 build plans for 50 different projects. Those plans have automatic branching per PR. Then I have one more Bitbucket repository marked as linked repository in Bamboo, where all plan specs for those projects are held. Now whenever I try to change something in any of those plans through updating specs, all plans that have active PR branches, are not updated.

Error message I get is: 

com.atlassian.bamboo.specs.api.exceptions.PropertiesValidationException: Plan branch / workflow: You can't change the default repository because automatic branch management for this plan is dependent on pull request  and PR plan branches exist for this build.Update plan's branching configuration or delete existing pull request plans to enable switching the default repository.

I have not changed anything about any default repository.

What I have tried is to push specs once and next times with generated repositroy oid, I have tried use exact copy of repository settings from Bamboo UI generated specs, I have tried different patterns of additional repository settings, all to no avail.

I don't know what it means by updating plan's branching configuration, since there is nothing that can be changed by me to keep required plan functionality. Deleting existing pull request plans is also not an option, since it resets build counter which is used for my software versioning and deployment(all automatic branches need to deploy automatically).

Linked repositories might work, but that would be last resort since it requires me to manually add/update something from UI, which removes the point of CasC.

How do I tell Bamboo, that default repository settings have not changed?

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