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How is your template/ directory structure set up? If an index.html template extends from base.html, Django will choose whatever base.html is in your root template directory.
Solution:
Either rename one of your base.html templates to something like base2.html and put it in templates/ alongside base1.html, or create new directories in templates/ to put the base.html files into.
For solution A, make sure you change {% extends base.html %} to {% extends base2.html %} in the appropriate index.html template.
For solution B, your base.html files would keep the same name, but be in different directories. So one is in say templates/base1/base.html and the other is in templates/base2/base.html. Your index.html files would extend like {% extends base1/base.html %} and {% extends base2/base.html %}. Note that all extension paths are relative to the root of your chosen template directory.
IMO solution B is better as it separates the code for each template base into different, explicitly named folders. Better organization/flexibility and less confusion for you in the future.