Guests say the system will not allow them to alter their stay after they have arrived. I haven't tried it, so don't know, but perhaps it was not possible for the guest to do anything but create a second booking to extend his stay. It was good of you to refund the cleaning fee for the second night. That was just through the resolution centre, is that right, @Samuel235? So it took only a minute?
It would be nice of the guest to review you, especially after all that, so if you think he might not, you could write him and ask. If you are low on reviews, it would not be out of order. When you say that if you don't review the guest it will affect your percentage, it appears you misunderstand the stats. Easily done, but percentage of reviews means reviews of you by your guests. We are not scored on how many reviews we write.
I have no recommendations, though. This is just something that sometimes happens.