It shouldn’t have done so, but perhaps I misunderstood. My assumption was that you did the update to 2.0 on Snow Leopard a while ago and have worked on the project since, and that the division of chapters and all the added research documents happened after the upgrade. So all of that never was in the original 1.x project at all, but rather in a new 2.0 project. When you updated on Lion, you used the old 1.x project, which hadn’t been touched in however long and didn’t include all the work you had done in 2.0.
All projects that were created in 1.x are going to need to be upgraded for use in 2.x, due to file format differences. Once they’re upgraded, you can’t work on that upgraded version in 1.x any longer, but when you make the upgrade, the first step Scrivener does is to make a backup of the 1.x version. So at the end of the upgrade you have two copies of the project, one still in 1.x format and one in 2.x format. They’re completely separate at that point, so work done in 2.x doesn’t affect the 1.x copy–and likewise, if you open the 1.x copy in your older version of Scrivener and work on it, those changes won’t exist in the 2.x copy.
As for Lion’s versioning, it’s not really intended for program types like Scrivener that have to synchronize multiple files for a project, so there are no plans to integrate that. Keith wrote an explanation on it here.