Emptying and scrubbing out your pond is a very bad idea. It should only be done if your pond has been contaminated by some kind of chemical or infested with some type of disease you can't get rid of.
As mentioned, it's stressful for the fish, but more importantly detrimental to the pond's ecology.
As your pond matures, nature forms a biofilm all over everything. This biofilm helps with the natural filtration process, plus it hides your liner. Beneficial bacteria also colonizes inside your filter. If you home's water is chlorinated, you should rinse your filter with pond water. The chlorine will kill the beneficial bacteria.
There's a thing we call new pond syndrome. It happens when you start a new pond. The water can turn green within days because your natural cycle hasn't matured yet. The green water is due to an algae bloom. Since the beneficial bacteria hasn't colonized yet, there's nothing to fight the algae...thus, green water.
So, every time you clean out your pond, the cycle has to restart. It can take weeks.
So, it's not just the mechanical part of your filter that cleans the water by catching solids, there is a biological process that goes on in there too. And that biological process is going on all over the place in your pond. All this good stuff is being killed off when you clean out your pond.
I never do water changes. I let nature do it when it rains.