I'm planning to re-format my main PC soon; I built it about a year and a half ago and I want to get a fresh start. That said, I've got a pretty decent catalog in Lr and I want to ensure that I maintain all of those images, edits, etc.
Let me first explain some madness (possibly)... I use a CF card reader and manually copy/paste images from the card, to a directory on my HDD. Once that is complete, I go into Lr and manually add that folder to Lr view viewing/editing. I wanted to explain this, because I have no idea if it changes the export process at all or not.
That being said, I'd prefer to be able to export everything in a single effort if possible, but I assume that I would export each folder if I had to... I'll certainly be testing this (probably to my laptop) before completely wiping the PC.