The Atlantia was a Mercury class Battlestar introduced 16 years after the Cylon war. Atlantia was only the second such ships to be commissioned and served for twenty years in the Colonial Fleet. For the first ten years of service the Atlantia was one of the Fleets primary ships of the line. Following this she was named the Fleet Command ship.
The Atlantia is said to have been de-commissioned four years prior to the Cylon attack. However, this contradicts the previous mentions of the ship. A few months after the start of Operation Outreach Atlantia is said to be involved in a patrol duty along the "Red Line" (possible meaning the armstance line with the cylons). It is possible that the ships decommissioning was delayed. A while after this it is reported that the the Battlestar "Atlantis" was being assigned as one of the rescue ships for the Prometheus. If this was in-fact a typo, this would be her last assignment before her final decommissioning and replacement with the Nova Class Atlantia.
It was on this Atlantia that William Adama made his 1,000th Viper landing and received the promotion to Major. At one point in his career, Galen Tyrol also served aboard the Atlantia before being assigned to Galactica.
The confusion regarding Atlanti(a/s) and the time of decommissioning is simply a mistake. In one comment Ryan implied that the mistake was one that would be cleared up in any future revision of the story and that interpretation is up to the reader until then. Prior to episode 3-10 the idea was that Atlantis was merely a mistake by the media ("Atlantis" was intended to be the "Atlantia"). Now it can be assumed either that the Atlantia's decommissioning was delayed until shortly before the launch of it's replacement or there is another Battlestar with the deceptively similar name "Atlantis" (and that the mention of Atlantia patroling the "Red Line" was meant to be Atlantis).