I bought FE from stardock, then upgraded via steam. That shouldn't matter if they do their job right....
I'm not sure I follow you, you can download and install from stardock.com whenever you want. How did they not do their job right? Even if you got them both from Steam, there is no "upgrade", they are completely separate installs, whether you got both from Steam, or one from Steam and one from Stardock.
If you never un-installed FE, it should still be on your computer, ready to run. FYI, should be a new update for FE soon as well.