I am surprised you have not read about Operation Trident. You have a forum member here, niaz sahab, who was present on station during this, if I am not mistaken.
http://defencejournal.com/may98/fightergap2.htm
The Air Force provided air support to the Navy at Karachi, on a report from a PIA aircraft flying reconnaissance for the Navy, the morning CAP (combat air patrol) at Masroor was asked to investigate, the result was that PNS Zulfiqar took 900 hits of point 5 inch ammo killing several officers and men, with many more injured.
The ship was at anchor, it was not going anywhere! Had the pilots not been so trigger happy, the ships identity could have been established with just two radio calls, and had the pilots had been trained in ship recognition they would have reported back that it was the PNS Zulfiqar!