Just done a clean install and things seem OK now. I'm a little concerned about why my storage drive disappeared (that's what caused all my apps and stuff to disappear). The drive was visible in DSM but there were no mounted volumes and it wanted to format the disk to create them...
Yes, I had the same problem! Everything was working fine... I shutdown DSM, booted it back up and suddenly everything had gone. All my apps wanted repairing and stuff...
The only thing I can thing of is DSM perhaps automatically updated or something. I am going to try reproducing this again. Otherwise I will be certainly concerned if this was to happen again!