Locked Folders Lost after Lion Upgrade

I bought my MacBook Pro last year. It shipped with Snow Leopard. Since then I have been using File Vault, and within my Library folder, I had one main folder, a sub folder, and a sub-sub folder locked. Never had any problems accessing those folders. Yesterday, I upgraded to Lion and now the "Library" folder does not even show up and is unsearchable. *** happened and how do I recover it?

I tried turning off the Legacy File Vault and it required more disk space than I had available on the main hard drive, so I cloned the HD onto my LaCie 4TB Thunderbolt drive, making a bootable drive, re-booted from LaCie, and de-crypted it on there. This did not make my folder re-appear.

Do I need to revert to Snow Leopard in order to see that folder again? De-crypt and then upgrade to Lion? Please help.