As BustedKnuckles said the codes are still in there, but they will be “history” codes. Not all scanners will read them, including many of those at auto parts stores. So if you give an AP store a shot call around first to see if they can scan for history codes. (They still look like “P1234”)
I like BustedKnuckles guess about the moisture & the wires. How old are the plugs & wires? You can do a couple of simple things to investigate. At some point when it is dark, pop the hood and start the car. Watch for any signs of a “light show” around the area of the plugs, wires, and coils. You could also take a misting bottle with water in it and mist the wires with the car running. If misting the wires makes the engine stumble then you’ve likely found the issue.