FAA Action  

I and 3 other pilots at my base had a letter put on file due to an over flown transponder inspection ( this was around 2007 . I spoke to FAA about it as I thought it was unfair because at the time we had a one sheet maintenance update, so we were unaware. The company got fined by the FAA. I think it was around 25,000 and they told us it was no big deal and we shouldn't worry about the letter being put on file for each of us. I called them on the anniversary two years later in Oklahoma, to confirm that it was taken off of our record which they confirmed it was. but even so when I interviewed with Air Methods in 2010 I still told them about it just in case and they thanked me for my honesty and agreed that it was not a big concern and that many people get such letters us put on file.

so I would say that yes, they do delete the file after two years, but to be on the safe side just explain your side of the story, and I would believe that most companies would understand that you did not need to tell them, especially if it's gone past the two-year mark and at the end of the day honesty is the best policy at least for me It has been and I have been flying HEMS for 20 years. 

i know it will hurt you personally but I  believe it will not hurt you professionally.