Ok, generally, in Applications, we recommend NOT stopping the main spindle or subspindle for tool changes. This is for several reasons -
A) Cycle times will increase by at least 20% as the machine will now have to wait for the spindle (s) to get up to speed, even with a fast acc/dec like the Puma, it's still adding precious seconds to your part times when you should be decreasing them. Same for things like coolant pumps as many times the machine will "wait" for confirmation that a particular function is operating before continuing on.
B) The start/stop on the spindle is placing a great deal of stress on the motor (s), Drive (s), belts and bearings. Watch your motor load meter when the spindle starts/stops and you'll see it peak at VERY high levels as the motor tries to crank the spindle to the correct speed. However, once running, you'll see that motor loads stay fairly steady and even paced, all the way through the speed range.

10,000 parts on a spindle. I feel that perhaps more data is needed. Was the machine involved in a turret/workpiece or turret/spindle collision? Are workpieces/workholding weights at or over the maximum specified? Are cycle times very high with hours of hogging?