Yes, the frame (especially the area where the fender fits) changed in 2007.
The inner fender (the structural part that the cosmetic outer fender attaches to) is shaped different in 2006 than the inner fender used in 2007 and 2008 even though 180 tires were used for the VRSCD in all those years.
If you look at the parts catalogs for those years you'll see the difference. (Here's one of several sites were you can find most of the Harley parts catalog diagrams from 1979 to 2017.)