@mikeconnolly,
I'm not saying this will do much good, but sometimes a channel is lost and then a few weeks later when I do the Auto Scan it comes back. (Re-Auto Scanning has returned signals on a new number.) Plus, with a digital signal, if there is a physical object between the digital signal and an antenna, the signal is kaput, as far as I know (I thought the digital signal is just "line of sight"). Meaning, any new buildings, out of one's view, could be messing up the signal.
Is it possible that the lost channels were put back on an analog signal, not digital, and your tv wasn't scanned to pick up analog signals?
This is what I call progress in the 21st century.