[jar]

Will this work, I know both bikes are 200mm rear

 

[Greaseball]

I think it should, so long as the Fat Boy fender is from a pre-'08, 200 tire bike.

 

[Rollmeaway]

The 07 Fatboy uses frame # 47687-06A
The 06 FXST uses frame # 47687-06BHP

My guess there is a slight modification done to the BH Standard frame marked P that will differ from the fatboy but you could almost bet it won't prevent ya doin the swap.

It wouldn't take much more than a call to the parts counter at your local dealer to find out the diff. Their parts catalog should list the preceeded #