It depends on what you cross-polinate. If you're only cross polinating the common plants to get better blooms, then you should be fine. I've been manipulating the clock in my game and I only have the green soil. It's not a good idea to try and cross-polinate to get the more rare plants until you've got the better soils, but it will work with the green soil.
Try this: Plant your seeds, then set forward an hour. Re-water prune as needed. Pollinate everything, then set your clock forward another hour. Your plants should stay healthy enough to at least harvest more seeds, especially if you've tried to grow them in soil that's not healthy enough for them. I've been using this method for days now, and it's helped me earn some great money.