If they do retroactively add non-Chiss jokes for Chiss in the Smuggler line, then I'd really consider that Bioware would actually give thought to having retroactive companion SGRA's. However, I am going to assume they'll only have the two obligatory "I think you're pretty/handsome" options on Makeb that lead to sod all and call that "equality".
Yeah, it is always possible, but it is definitely more complicated that taking a few jokes and replacing them with another. I don't think they would go through the trouble to just add a few incomplete flirt lines to existing companions,, that would make more people upset than happy, which is why I think they'll go with new companions that they can start out from scratch with, and not have people worry about having already gone through all their current companions' conversations before a change was implemented.
I missed the word "companion", though I'm surprised you consider two [Flirt]s to be full blown romances.
How do you know it's only going to be 2 flirts? I don't think anything has really been revealed about it yet.