Can anything be done to placate owners in the case of last minute changes to a booking (where the booking is actually moved to another property)?

If you run a hotel-style environment, allowing guests to move about as they please and to change their choice of an apartment will inevitably lead to this sort of issue.

If you wish to prevent this from happening it might be worth training the staff to keep a note of apartments where bookings are 'moved' and they can then manually push a new booking that way next time to make up for it. While the system will do this automatically over time, it could avoid some of the disappointment.