My bunnies also have vinyl floor for their condos. I buy them these to cover the floor: http://www.pet-super-store.com/html/Snoozy-Sleeper-Mat.html
They are called “Snoozy Pads” and I buy them at my pet store (not sure if you have “Global Pet Food” stores where you are but I’m pretty sure most stores would carry them). They are made to put in dog crates and come in lots of different sizes.
I just bought one last night for Olivia’s new condo. If you can’t find one big enough you can use several small ones. I find they are very fairly priced. If bunny doesn’t chew at them they last long as well. I first bought one of these pads when my lop was experiencing sore hocks and they made a huge difference. Since he has a big one in his cage, he hasn’t had sore hocks again. I swear by them. They are very comfy, thick and stay in place. Although, if you’re bun is a chewer make sure to keep an eye that she is not chewing the pads but if you get one big enough for the whole condo, she will probably just accept it as floor.