It will have no effect. It only treats the water passing through it. And if you haven't replaced the bulbs in the last year, its not doing anything anyway. UV bulbs need to be changed every year.
Don't replace your beds fully until your system cycles. In fact it's not a bad idea to run the filters pre bed anyway.
Matt, do you if the UV lights (when used in that way) affect our ammonia oxidizing bacteria?
Wendell, you should be able to control the algae (at least to a degree which is wholly manageable) just by blocking out any excess light/sunlight from hitting your water. (At least I've always been able to).
UV lights are very efficient at sterilizing water. It first is used in water treatment plants in the mid-1960s by the EPA. It's still used today to sanitize human waste water processing plants. You can use it in your hot tub. Using the combination of UV irradiating and Ozone injection removes the need for using chlorine or bromine; however, you will never get a chemical company to admit that. I've made hot tubs with this method for 20 years with no problem.
UV lights are good for people who have a decorative pond and want to minimize clouded water. UV bulbs need to be changed yearly if running 50% duty. The cheapest place to get them is from a saltwater aquarium store. And the glass case needs to be made of quartz, not glass. The killing wavelength will be blocked by regular glass. It will slow down your oxidation of NH4 and in turn there will be less NO3 available for your plants. Please remember that killed bacteria/algae will produce more NH4, H2S and CH4 because of decomposition. Your pH will be affecting depending how much AP sludge you have at the bottom of your tank/pipes.
I'm assuming you are complaining about clouded water. If you have algae growing along the sides of the tank and the fish are not eating it, you may be adding too much food causing an NH4, NO2 and NO3 ripple spike. :-) This would cloud the water as well. My system is 5 years old with no UV sterilizer, in direct sunlight and the water is really clear. There are a lot of algae on the tank walls the fish eat. I have not fed my fish ever.