Let me understand this. The wheel motor shaft broke inside the hsg and you feel there's no debris?
The wheel motor displaces over 90% of the oil the pump supplies it. It goes in and it comes out back to the pump. So tell me, how is it possible nothing got into the pump? Reason being, I've never seen that happen.
Flushing won't help. Very, very rarely can you take shortcuts on hydro work. Suction and return hoses, oil tank, filter head and pump should come out and be flushed. Cross contamination usually does not occur.
Depends on the system, since there isn't even a brand posted. Don't and won't get into a debate over it. Do what ever you feel is needed.