What branch should the manual cleanup be done

Maintenance listed here: https://confluence.atlassian.com/bitbucket/maintaining-a-git-repository-321848291.html seems to make changes to the entire repo.

The steps rewrites the history and the updates the repo.

Could this process be destructive, will it affect all the other devs code in different branches within the team?

 

Just want to make sure before doing something drastic

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