Average identical sweeps or lowpass filter sweeps first?
If your are using a linear time invariant lowpass filter (such as a Finite Impulse Response (FIR) or an Infinite Impulse Response (IIR) filter), and have negligible rounding errors in each operations then doing the lowpass filtering before or after the averaging will yield the same results.
Note that from an implementation perspective, doing the averaging first would likely require fewer computational resources.