Good morning,
Try using Derived Components (See help for details)
In case you don't know how
1- Save you assembly
2-Open a new part
3-Press Return and delete Sketch1
4-Press on the Derived Components Icon
5-Browse to Your assembly and insert it
6-Save your part (You can break the link to your original assembly if you do not want your part to update with the assembly)
And Voila, now you can export to Stl.
Cheers,