Ok, I know it has been two years, but maybe someone will find this thread searching for a solution.
I had almost the exact same issue with my Octavia (the only difference is that my engine is BFQ), 16555-P0171 "System Too Lean" and misfires on cylinders 3 and 4 in addition to that. The story was that I've encountered misfire on cylinder 4 at somewhat around 238K km, decided to replace spark plugs and wiring (which seemingly solved the problem at the time), and then after another 1000 kms my cooling system suddenly sprung a leak, so I left my car to fix it at Škoda service for three weeks (the replacement tube required for the fix was nowhere to be found on local markets, so I've had to wait for original one to be delivered straight from the factory in Czech Republic).
And after these three weeks I try to drive away from service station, and car is trembling and wheezing, stalls at every traffic light, "Check Engine" goes on and off in random fashion – not good. Was a stressful ride home. After a check-up, VCDS showed exactly the error aforementioned.
As it eventually came to be, the source of this issue were exactly my "new" spark plugs, bought a little on a cheap side and, as I was told by my mechanic, only had one electrode, while original VAG plugs have four. We've installed the original plugs and she drove like a charm again.
Hope this helps someone!