In order to clean up unused phrases, you can use a specific command when pushing strings from your code to Transifex, that’s the —purge command.
Using that command you will keep only phrases that appear in your current code instance and delete everything else, e.g. phrases found on other active branches that are not synced with yours.
For more details, see the available push command options for the javascript SDK. These options are available in all Native CLIs in supported languages/frameworks.