I have few remote repositories configured for my project, whenever a new branch created it shows up under the remore repository, but when they are deleted later on, they are not removed from the list and there is no way to remove them unless I remove the remote repository and add it again
I am having the same issue. I selected "Fetch" then "Fetch from all remotes" and "Prune tracking branches...". Reloaded SourceTree and they were still there. I then tried to right click and "Force Delete" them but I get an error saying they no longer exist... I tried restarting SourceTree after that too and no luck :(
If anyone is still having issues with dangling remote branches following a fetch and prune, try deleting your project and then cloning it down again. Sourcetree then correctly located my branches in a different sub-folder (which was capitalized) and succeeded in deleting them permanently.
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