That's a tough one--seems like everyone with free ranging chicken runs into this at some point. Here are some ideas I've read from others and/or tried myself.
1. Do a mulch of large rocks. So, plant your flowers but then cover the space around them with rocks large enough the chickens can't fling them around and/or are discouraged from scratching there. This has worked somewhat for me, but it's amazing how strong they are when motivated to scratch!
2. Place overturned crates atop the plants. I did this with my pumpkin mounds and it worked beautifully. First, the crate protected the seedlings and then the vines grew through the spaces in the crates. I happened to have green plastic crates that kinda blended into the scenery. You might try this with big, flopsy flowering plants that need some support anyway.
If you had large baskets with spaces between--or could knock out a few staves of an apple crate, for example--you could do this with a more natural-looking item than a plastic crate. I'd recommend burying the crate or basket a few inches in the earth for stability.
3. Create an ideal location away from your flower beds. Observe your chickens and try to figure out if there's a particular reason they scratch in the beds--is it to take dust bathes, looking for bugs, eating a certain plant? Maybe you can give them another dust bathing site, or give them access to your compost pile to find bugs, or plant something just for them to eat.
When my flock began crossing the road every day to hang out under my neighbor's pine trees I created more shade in my yard and also began throwing out some treats over here just before the time they'd usually cross the road. It isn't perfect but after a few weeks I've nearly broken their habit.
Good luck! Those chickens are so fun and so frustrating all at the same time!
