I have gotten these "missing regions" where whole parts of my song disappear; even my BACKUP songs would also have the same disappearing regions, making a return to my old song impossible. This would only happen after I saved my project and re-open it later, just as you describe.
I have no solution to how to bring the regions back, but I narrowed my problem down to the following bug in the matrix editor, which I've documented in this thread:
http://discussions.apple.com/message.jspa?messageID=767597#767597
long story short, the problem occurs for me when I am editing multiple tracks in the matrix editor, upon which trying to drag/extend/copy/paste multiple parts at once will sometimes result in an error message. When you click "ok" it looks like everything is fine, but under the hood logic has had a major problem and when you come back to the same song, regions will be missing. The only solution I've found is to continue off an older, unaffected version.
Because of this I now "save as" frequently and avoid editing multiple tracks in the matrix editor (you can view them, but double click the part you want to edit BEFORE you edit it). Sometimes in the heat of the moment I forget and will edit multiple parts at once. When the bug happens, I export all midi data and re-open an older song, paste in the data and continue.
Hope this helps.