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When the Bitbucket Server URL changes, users need to delete and recreate the Application link. However, there is no notification of this requirement.

Please delete and recreate the Application link and re-save the Repository:

Go to Bamboo Administration >> Overview >> Application links
Delete the Bitbucket Server application link from Bamboo
Go to Bitbucket Administration >> Application links
Delete the Bamboo Application link from Bitbucket Server
Recreate the Application link – this can be started from either application and you will be redirected to the other
Re-save the Repository
If the Repository is still unable to connect, you may need to delete and recreate the Repository

Note from linked ticket BAM-18273:

If you have Plan Branches, these will need to be manually updated in the Bamboo database. To do this, please:

Run the following update query, replacing <old-url> and <new-url> as needed:

update VCS_LOCATION as V
   set xml_definition_data = replace(xml_definition_data,'<old-url>','<new-url>');

relates to

BAM-18273 Ability to bulk update Bitbucket Server/Stash repository URLs

Notify users of need to recreate Application link to change Bitbucket Server URL