This is really something that can only happen in the C-USA, MWC, and AAC championship games because those are the only conferences that host a non-neutral site championship game. The MAC and Pac-12 used to, but they don't anymore.
Times it's happened:
2000 -- Marshall hosted Western Michigan. Lost regular season, won Conference Championship.
2007 -- UCF hosted Tulsa. Won both games.
2012 -- Tulsa hosted UCF. Won both games.
2014 -- Boise State hosted Fresno State. Won both.
2016 -- Wyoming hosted San Diego State. Won regular season, lost conference championship.
There's really not a lot of factual basis to the whole "it's hard to beat a good team at your place twice" thing.