Sony Z5 Premium - MTN

Last year January I took a Sony Z5 Premium with MTN. In June 2017 I did a software upgrade and the battery drained out, after numerous times of trying to charge it nothing seemed to work. I took it in to MTN and they even tried but nothing seemed to work, that's when they said that they will have to book it in to Sony. to my surprise Sony comes back to me and says that I will have to pay R4500 to repair the phone! Repair??? All I did was an upgrade on the software , to my surprise the technician says that the mother board has to be replaced and because my back chrome cover it cracked due to negligence on my side 6 months after taking my contract. I do not think it is fair for me to be carrying the cost for a software upgrade that damaged the phone, further to that I am paying for a contract with MTN for a phone I don't have.