This is why it's very important to keep plants growing in your tank. If it's time to replant, simply pull out as much of the dead plants as possible. No need to clean the rocks or be super picky about getting out all of the roots. If you do clean everything completely though, be sure to add more Zymbac (beneficial bacteria). Afterwards, plant new seeds on top of the grow stones. I like to put them on top of a piece of coffee filter to keep them from falling through. Also check the back of your seed packet for additional instructions (most sprouts need to be rinsed clean). You can grow various plants with the Water Garden including sweet potato leaves, green onions, and various house plants. Here's a great article on re-growing plants that you may already have in your refrigerator. Scallions are super easy to grow in your Water Garden, as are transplants of cuttings you've made yourself.
If you need to change the water because you have multiple fish or just want to clean the tank, here is a helpful "how to" video. Again, when changing the water, it's important to replenish some of the beneficial bacteria by adding more Zymbac.