I think so, but can't test it right now.
Thinking FBC or DDT, or even plain old FSC might do it. If not then it should be relatively straightforward to code an iterative loop to do the job.
Questions :-
1. How big are the files ?
2. How fast do you want the comparison ?
3. How frequently do you want the comparison ?
4. What results do you need ? (i.e. do you just need to know they are the same/different?, where the differences are ?)
One technique I've used before, when I need to find a bit set in a BOOL array, is to COP the BOOL arrays into DINT arrays, use FSC on the DINT arrays, looking for the DINT <> 0, and then drop into another routine to find the bit set in the DINT.
The .POS of the FSC, multiplied by 32, plus the bit number tells me the position of the bit set in the BOOL array.