Not really, flushing will just add more water to the system and if there was water in the ducts to start with, flushing will just add more as it’s likely there is no way to eliminate the water from the ducts. The prevention to this situation is to use drains at all low points and keep them open until you are ready to grout. The thixotropic grouts will do a decent (but not perfect) job of driving the accumulated water out of the ducts – the best solution would be to continue pumping grout (I know, that’s a lot of extra grout) until the density readings improve – and they will as the grout pushed more water out of the duct.