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? I have an early-2011 MacBook Pro 15" with a 128GB SSD. I replaced the built-in SuperDrive with a 750GB MCE OptiBay HD, so my boot drive is the 128GB SSD (speed!) and I have moved over most of my Home folder except for Applications and Library to the 750GB HD (storage!). To make it all work smoothly, I followed TUAW's advice found here.

My directory structure looks like:


SSD (Boot)

Applications
Developer
Library
opt
System
Users

HD (Storage)

Desktop
Documents
Downloads
Dropbox
Library (the other one)
Movies
Music
Pictures
Public
Sites



So, my concern is that upgrading to Lion will eradicate this structure in some way and that I will have to do a special install. Has anyone tried this yet and can you tell me if there are any pitfalls I need to be aware of?
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!