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Accepted Answer
What files are located in /etc/apache2/sites-available/
The presence of a .save file makes me think that you may have used an editor to modify your 000-default.conf file which created a backup (as the .save).
If the configuration in your 000-default.conf file looks correct you should be able to safely delete (or move somewhere else) the 000-default.conf.save file and try the renewal again.
FInally, after two hours of struggle, I landed on this page and this was the exact problem. Just deleted the .saved file and the renewal worked.