Here is the official announcement of the two versions on our website, but here's the part you're interested in:
Improved Stability Through Multiple Releases
FlexSim 16 Update 1, which was released on June 22, is a landmark release because it offers—for the first time—the option of two software versions. If you use FlexSim 16 Update 1, you’ll receive the latest features and bug fixes just as with any new release of FlexSim. But you also have the option of choosing the stable branch of FlexSim (16.0.2); this long-term release will continue to receive bug fixes introduced in subsequent updates without the new features, giving you maximum stability. And when FlexSim 17 comes out next year, a new long-term release will be available with all the great features that appeared in the various updates to FlexSim 16.
So 16.1 is the newest version with the newest features. 16.0.2 is the latest bug fix for the long term service release (16.0)
Matthew Gillespie
FlexSim Software Developer