I think I may have a similar problem to which I need a solution. I am running moodle 2.4 on a virtual private server at Inmotion hosting. I am running into problems as my server is full. This was a surprise, as I am only hosting 2 classes.
I investigated the problem, and it seems that the "eraser" is not deleting old backups that have been "deleted" through moodle.
I think that the problem is that when I originally installed moodle, I named the moodle data file "moo" instead of allowing the default "moodle_data." (don't ask why I made this choice, it is a long story)
The automated backups were working fine until I ran out of space.
I thought a possible solution might be to go to the automated backup setup and "specify the directory" for the automated backups, to help the "eraser" find them. I searched through the moodle data file hoping to find a single directory where the backups were stored, copy the path, and then enter that in the automated backup settings.
Unfortunately, it appears that the backup files are being stored all over the place, making it difficult to figure out to what to set the "specified directory for automated backups."
I can find the backup files in the database, but I am not sure what would happen if I simply deleted them. I don't know how moodle might react if a database file were simply deleted. Right now, I have a small file, 50KB, that I am using to overwrite the backups. Moodle seems fine with this, as there is still a file with the correct name in the data base in casemoodle should ever look for it.
Another option would be to help the "eraser" find the files be leaving the automated backup settings at default, and then just rename my database to the default, which I think is "moodle_data". I could then go into the "config.php" file and change the path to the data file, but I am not sure if there might be any other place where a change would need to be made.