Yes, never a good thing to get grit into the engine.
It will cause premature wear.
An easy way to flush the oil passages ….
With the drain bolt removed, pour a good amount of either diesel or kerosene down each oil passage and let it wash it down and drain out of the oil pan.
As to the water jacket ..
Remove the thermostat after the engine is reassembled, leave both upper and lower hoses off the radiator and run clean water through both the upper hose then the lower.
Doing this should get most of the debris out.