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Bamboo seed rerun is wiping out all the branches from the plans this in turns reset the history of app build versions and re adding the branch will create a fresh artifact version in bamboo and it will conflict the the version that is already upload with the same number.
Please find screen shot of different configs for the plan for branch cleanup
Bamboo Plan DSL
Vendor:Mibex Software GmbH
Thank you for contacting us. I'll respond to the ticket. Please feel free to close this question.
Michael (app vendor)