Engr - no first hand knowledge here, but s/w can indeed protect a system from a lightning transient, depending on the nature of the lightning transient. The example I saw was for something called "multiple burst" - as it was explained to me lightning strikes are often made up a very rapid series of smaller electrical pulses as the strike finds it's way to the big strike (this would probably make more sense if I could draw it for you, but think of a series of small sparks connecting into one massive spark). The problem is, those smaller spikes can mimic a the wave form of a valid digital electrical input - and the LRU can't tell the difference. The fix was to change the software so it could differentiate between actual digital inputs and the lighting induced inputs.
In a way, it's ironic - as an industry we've spent decades convincing everyone that lightning wasn't a big threat - we design for it. Except that isn't entirely true - we can't always protect from the most severe lightning effects. For example, we protect the engine control from the electrical transient, but if the lightning attaches to the inlet the shock wave into the inlet can cause the engine to surge and flameout (yes, it's happened). There was an event roughly fifteen years ago (memory says it was a 767, but don't hold me to that) where the lightning attached to the aircraft nose - the resultant electrical field around the flight deck incapacitated one pilot (the other pilot was 'affected' but fortunately was still able function). The bottom line is we can design for the lightning effects, but we can't completely protect for the worst case strike. We still need flight crews to do their best to avoid it...
BTW, shortly before I retired, I was on a 747-8 flight test when we took a major lightning strike - I was in the flight deck at the time and it was quite a shock (emotionally, not physically). No adverse affects to the aircraft systems, but it did significant airframe damage. But what I really recall is the flight crew's reaction to ATC - basically ATC had put us into a spiraling decent right in the middle of a cell until we finally got hit - and the flight crew didn't appreciate it...