I once had a hassle with UA: they claimed that I checked in for a flight, but never flew, and thus would not receive credit. I had in fact flown the segment, but maybe a gate agent didn't scan my boarding pass correctly or something -- UA remained quite skeptical about my claim that I'd flown the flight, and only granted me the miles "as a one-time exception." So, on UA, one-time exceptions aside, checking in and not flying won't do it.