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The plugin has not changed since 8.0.1. Please make sure it's enabled.

For what it's worth, I was updating my development and test sites on my laptop just an hour ago — I hadn't touched it for two weeks. The test sites are all running Akeeba Backup Professional 8.0.6, I did see the backup on update message above the Joomla Update page and the backup before the update did run.

If the entire folder is missing the only explanation is Joomla failed to copy the updated files the first time it tried installing the updated version of the plugin (packaged with the rest of the extensions included in the Akeeba Backup package). This is one of the issue I have been reporting to Joomla for years (I first saw it around 2007, when extensions updates became possible in Joomla). I have seen it with other extensions too. It's proven very challenging to reproduce which is why it has not been fixed yet.

I have a hunch on where it might stem from but I can't figure out the conditions to trigger the problem so I can demonstrate it and get it fixed. When Joomla installs an extension update it deletes the files and folders included in the extension's manifest file (the XML file). Then it copies the new version's files over. If there is a failure in file copying there is no rollback; the original files are already deleted. It's also possible that there is no error displayed. The only way I can think of triggering this issue is having the Joomla temporary directory contents deleted in the few short milliseconds to a few seconds (in the single digits, even on slow shared hosting) between Joomla starting to delete old extension files and starting copying the new extension files. So my best guess is that this is perfectly possible and can be reasonably explained but extremely rare and hard to reproduce.