More data please. Exactly how are you "changing the filenames"? I can think of a number of possibilities immediately, all of which should work perfectly.
1. You open the part file and do a Save AS.
2. You do a Replace.
3. You edit component properties (slightly different issue, but could result in different names in the tree).
If you are changing file names in Windows outside the assembly and expecting SW to magically realize you have done this - ain't going to happen.
John Richards Sr. Mech. Engr.
Rockwell Collins Flight Dynamics
There are only 10 types of people in the world - those who understand binary and those who don't.