You will be fine. We have gone to WDW and flew standby for a different flight than what was on our ME travel documents and we had no issues. Just tell them at the ME check in counter and they will make a note on your reservations as to what flight you flew in on.
No need to worry. Trust me. We once took a bump - gotta love the free future flight vouchure- and when we got to the SSR we walked by the luggage room on our way to check in, and saw our luggage in the luggage room. It had arrived ahead of us seems our luggage did not get bumped from the orginal flight. So we told the CM who was driving us to our room and he went and retrieved our luggage and put it on the golf cart with us.
So even if you documents say one flight number and you actually fly on a different flight you will be fine.