Yes and no... That is why you need to make sure your soil has enough perlite in it, to really take aggressive flushing (among other things). It makes the water drain out much much faster, so the roots don't drown.

But if your soil is heavy and either too clay or too organic matter, yeah, you can have issues.

And obviously if you have no drain holes that is a problem.

And you can flush any time. But I would then give a little weaker nute solution on the next watering.