Sorry to hear that you deleted the wrong images. Hopefully you can recover from a backup.
Good news. It boots! I haven't tested the encrypted folder yet but will get to that soon and let you know.
Not sure about one thing. I noticed lots of disk/Green light activity. Since booting, its almost constantly on, for 25 mins so far. Funny I also noticed that on the vanilla LE12 image too. I didn't take it seriously since I was just testing out the LE12 image but now i'm wondering whats going on. Safe to say its an LE12 problem.