What are the exposure times, out of curiosity? I can see a couple of scenarios... Minor differences in exposure times to deal with 'minor' environmental changes... Maybe one night is clearer, darker, or halfway through the night you realize the exposures can be changed, etc.
The other situation is to target particular sections to either avoid overexposure, or allow it to gain signal in faint areas ... In other words, objects with high dynamic range. M42 is the classic example. In this case, you would likely be better off processing each set by exposure time and integrating the masters using the HDR composition tools.
Brian