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Why running fetch on command line doesn't update branches on SourceTree?

Edited

I have a script that finds all submodules on a repository and all base repositories, and runs a fetch --prune on them. I get notification of many branches being deleted. When I run the script again, it doesn't show those branches anymore, so they get updated.

I have SourceTree opened. Those branches are not deleted. only when I run a Fetch inside SourceTree they dissapear. If  restart SourceTree or press F5 it doesn't happen either.

How come this is happening? It's the same repos, the difference is that I use the SourceTree git from command line to do it.

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