Yep - they do it all the time. I think my original AU1 XR8 had 3 flash upgrades in about 6 months. It should cost nothing (or at least it should be part of the service cost). Ford only do it when a "fix" to the ECU is required - if you want it done at your request, then they may well charge for it, but don't let them charge more than 30 minutes worth, as it should not take any longer than that.