In fact your luggage is more likely to arrive as it will already in the bins whilst everybody else is still checking in. We had a stopover at LGW 23-24th Dec 2013 when all the electricity failed due to flooding and there were very few flights on the 24th and total chaos. We were on the only flight to EDI that left that day, eventually. We got on the plane to be told only 6 bags were loaded for the whole plane. We got to EDI and our 3 bags were there. (Still cant win the lottery though)

So getting them into the system early works