Looking at my own historic data, I still have the loan accounts (closed) on file but no schedule associated to them but still have all the other finished schedules. So it seems, I have solved the problem the same way (deleting the schedule when the loan is paid back in full). If you feel there should be a direct possibility via the UI to support this, please feel free to create an entry on our bug tracker and make sure to set the severity to wishlist. A cross-reference (link) in the description of it to this entry is very much appreciated.