Q: Have possibly been driving for a year without an air filter

I have an aftermarket K&N air intake system in my truck with a permanent conical air filter that requires cleaning as needed (estimated every 50k miles). I haven't noticed any drop offs in power or fuel efficiency, so I've never bothered opening up the box that it sits in to take it out and clean it. About a week ago, the check engine light turned on, and the Traction Control System and Stabilitrak started turning off for short 5 or 6 second bursts. When they turned off, the truck jumps when changing gears, but it doesn't happen all the time (typically happens 2 or 3 times on my drive home, a 40 minute drive). I brought it in to Autozone to get the check engine code and it came back as P0171. I decided to try cleaning the air filter. When I opened up the box that contains the filter, the filter's clamp ring had come loose and the filter was just bouncing around loose in the box. Thinking back, there was a clicking sound that started up over twelve months ago that I couldn't ever reproduce. I'm thinking that it may have been the filter bouncing around. If I've been driving around without an air filter for over a year, I'm concerned about potential dirt that's gotten into the engine/sensors that may not be working properly from getting dust on them. Is there anything I should do to clear out any dust that's gotten in there, or should I just put the clean air filter back on and let it be?