Hey buddy, the water pump is completely separate to the timing chain cover, either when you flushed the pipes out it overflowed out of the water jackets and into the timing chest or you have dislodged a partial blockage that was sealing up a crack. either way you will now have a sump full of water, so you will need to drain the engine oil. If you are unsure whether you have a leak or not you can fill the water jackets in the block up and leave it for a few hours and then recheck it to see if the level has dropped mate.
