Don't worry - the storylines for each patch are just a continuation of the '2.0' story - and the first story quest for the 2.1 patch picks up from the same place the 2.0 story ended - same as the 2.2 patch story picks up where the 2.1 patch story ended, etc etc. It basically continues as if there was no difference.

They're also identified exactly the same way as the 2.0 main scenario quests (with the 'meteor' icon) so you'll be able to know where to get it when the time comes.