What are the consequences of upgrading to OS X 10.7 Lion if I have a separate Boot Drive and Home folder drive in my MacBook Pro?
You probably should do what BMike has said as a precaution, but what you could also do is create alias folders in the Empty Users Home folder on the SSD. The alias folders would be empty, but would link to the actual folder on the larger hard drive. To create the alias, drag the actual folder to the users folder on the SSD whilst pressing command and alt together, you will see the green plus sign on the folder turn to a little curved arrow, whilst you're dragging.

Anything you put into the alias folders will go in the corresponding folder on the larger HD! This should also prevent any issues with the Lion upgrade, however in saying that, you shouldn't have a problem anyway as all the OS files are on the SSD!

Hope this helps!