Unless the settings had changed while I was away....i did not touch anything. I shut the program down before I left and when I opened it up they were gone.
Do you have a backup of the catalogue taken shortly before you went away? If so it would be worth taking a look to see if the missing images/collections are in it.
The only other thing to suggest is that sometimes odd happenings can be corrected by renaming the preferences file so that LR creates a new one. If it makes no difference then rename it back.
Or, you might just have to work your way through your images adding the relevant ones to the collections again...