Akeeba Backup will only delete the backup archives it knows about. This means that it will look in your site's database for other non-obsolete backup records taken with the same backup profile. Any backup files from that set of records matching your quota criteria will be deleted.
There are very good reasons we are not blindly looking into Dropbox or whatever remote storage service you might be using.
For starters, looking into the remote storage is orders of magnitude slower. Looking into the database takes less than 0.1 seconds. Looking into the remote storage takes anywhere from 2 to 50 seconds. This is the difference between running to completion and having the backup process killed because of a timeout error.
Moreover, you may have multiple sites or backup profiles send similar-named backups into the same remote storage folder. If we looked into the remote storage we'd be deleting other backups we shouldn't be touching. Not to mention that you might store your backups inside a folder with unrelated files or folders. You wouldn't want us to delete everything in your Dropbox by accident, right?
So based on your settings only backups taken on the same site, with the same backup profile, which still appear in your Akeeba Backup "Manage Backups" page will be removed from Dropbox automatically.
Nicholas K. Dionysopoulos
Lead Developer and Director
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