So basically I've had a pond for years, I know the ins and outs but things went south. Pretty sure I got parasites, thought they were under control after losing half my fish, but no. I can't see but 2 now and one is dying. At this point I just want to empty and and start over but I want to make sure I get everything clear of whatever was in there. How long do I need to let it set empty? I k ow I will have to thoroughly clean the pumps and toss all my plants so any advice on cleaning would be appreciated. I'm super bummed so I just want to know how to clean it and start fresh- it wasn't the water quality or anything like that and repeated treatments didn't help.

I had a koi pond for 35 years. And it is all about filtration, filtration, filtration. If you use quality filtering, including U.V., parasites should never have been much of a problem.
In 35 years, I lost 2 koi. Only two. Plus there is a tonic like chemical that you can use which should help. If you keep their immune system up, they should fend of any parasite.

Does you pond have a plastic liner?
How big is it but I would let it sit for several months depending upon size and type.

I hate it when stuff like that happens. Why do you think you have parasites? Beyond water quality, there are other things that cause fish to die. Where are you located? Have you added anything to your pond recently? Are your friends using it as a wishing well?

Assuming parasites, before you toss all your plants, figure out what parasites, vectors and where they came from. Are they external parasites like dragonfly larvae? Or internal? A lot of internal parasites have one part of their life cycle in snails. Did you inherit snails from someplace?

The fish were flashing. They would get dropsy and then be gone within a day or 2. I treated with an antiparasitic for a while and it helped temporarily. 600 gallon above ground pond with 2 pumps and filters. I did get snails somehow, I guess on a plant.

My pond was 1,500 gallons, roughly 13X8 and 28" deep. I bought it as a package deal. BUT it took me about a year and a half to realize that the filter that was included was undersized!!!
And not by a little.
Eventually I had a separate pump to filter water through a U.V. Light enclosed inside a plastic housing. The uv light took care of all of the parasites. Like I said, I lost 2 fish in 35 years. If you don't have one, you are just shoveling you know what against the tide!!
Then I had another larger pump circulate the water through a box filter. It had a compartment with three upright foam inserts. One was coarser then the two finer ones. Then another compartment had red lava rock in a compartment that was 16"x 10"x 8" deep to the best of my recollection. These materials worked together. Beneficial organisms colonized every surface aiding in keeping everything clean. A biological filter is what I called it.
Every spring upon start up, the filters took about a week to make the water crystal clear. I could tell if a dime sitting on the bottom was heads or tails!!! When the pond was running full swing in the summer, I had to clean the box filter (lava rock and sponge) once every week to ten days.
Now this is KEY, with the undersized filter box, I had to clean it almost every day!!!
I can just about guarantee you 110% that if you are having fish deaths due to parasites or whatever, it is because of water filtration. No doubt in my mind!!!!

My fish capacity was about 15 Koi, about 150" worth. I had long tailed and regular comets in there, about 3 dozen or so for about another 125" worth.

I have never heard that UV will kill the parasites too, I'll look into a UV filter. Like I said I have 2 pumps with filter (then those feed into a sort of mini bog style plant filter) and one of them is technically large enough to handle the load but I put in a second one once the fish starting really growing and multiplying. The water is actually very clear. I really don't want to, but if it comes down to it and I do just start over, do I empty thr pond and let it set out dry for a while? Or just cleaned out with fresh water?
No visible parasites but with the water quality being good on weekly or more frequent checks and them flashing thats my only guess.

First of all, with most parasites, they start out very tiny. You would never see them.
All kind of places use ultraviolet light to kill germs and to sterilize things. It will do that for your pond. If you buy one and run the pond water through it, you will not need to break down the pond at all.
When fish flash, they might have parasites in their gills.

So I got a UV filter and things are not going downhill fast- 2 that were already looking bad died- but another fish that was fine died pretty suddenly. So that means my water parameters are normal, filtration is above what is needed, and now I also have UV filter. So what is happening? Was that guy maybe sick but I couldn't tell? He died months after i put in the UV.Is nothing working? I'm bummed I thought UV was the cure.

I have no idea and not a lot of information to go on. Without a necropsy, you can't say for sure what killed him or them.

On Long Island, Zone 7, I had my goldfish and koi go foodless from roughly mid October through April 1st. And when I started to feed, it was with fortified wheat germ pellets. As they awaken from their winter slow down, that's all my fish could digest. Their immune systems are surpressed. I did not feed a regular diet until the water temperature reached the mid 60's.
I followed the reverse process in the fall and by mid to late September was feeding wheat germ pellets again. When the water went below 50 degrees Fahrenheit, I stopped all feeding.
Once the ice was off the pond I had the biological filter cranked up. The UV filter ran from late March until early November. Then I remove the bulb and stopped the circulating pump. The UV filter requires a new bulb every year.