Problem with files lists in QSF.

My first recommendation is to not do this. If the have different contents they should have different names. Your code can then use a generate statement or something like that to call them out.

The .qsf is not a script, just a location that stores assignments. You could do a pre-flow .tcl script that adds the correct file to the .qsf and removes the incorrect one. This would have the issue in that there's almost no way to tell which one was loaded on a particular build(without searching the .map.rpt to see which one was loaded in)