Jossed: As it turned out, Celestis is not some kind of alternate dimension. It's just a planet.
Schedule Slip: The Ark of Truth (and Continuum) was originally intended to be released during the Fall of 2007. Due to production delays, it wasn't released until the Spring of 2008.
This delay caused problems for Stargate Atlantis, which added Carter to its main cast in Season 4. They couldn't directly acknowledge the film's events until Season 5, but some spoilers were unavoidable.
Suspiciously Similar Substitute: It didn't actually happen in the end, but the producers were prepared to substitute the Doci in case Julian Sands couldn't reprise the role, rather than just cut out the character.