You should be able to create a new, updated index template that apply to all indices that starts with the pattern project-*. This will apply to all new indices being created, e.g. project-1017.11. If you then reindex the content of project-2017.09 into project-2017.09-1, the template will apply here as well. You should then be able to delete the project-2017.09 index and once this is done create an alias project-2017.09 that points to project-2017.09-1. If you are primarily querying through Kibana, the new index will still match the configured index pattern and you may not even need to create the alias.
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