Thanks, it's always good to have more info.
As he has actually regressed, and it seems to be related to last litter mate leaving, and if she does want to keep him crated at night, then the issue could be more complex. Although i understand the advice about making the space smaller, it works on the theory that dogs don't mess where they sleep and unfortuantley this little guy is doing just that!
IMHO I would go back to normal size etc.... just a thought, are all the dogs together at night (not in the same crate! But same room) or was he on his own at first, after brother went? As it could be a sort of anxiety. Also is it possible his mother has previously been cleaing up after him? Has his food been changed so he is drinking more?
Check nothing is scaring him, such as fridge buzzing etc. Thorouglhy wash all bedding with a biological washing powder as this will get rid of any lingering scent which says it is OK ot go there. Don't use disinfectants as many smell of wee to a dog! :D
I would take him for a health checkup as he has actually regressed. If no-one else can help and there is no improvement then I would in this instance recommend a reputable behaviourist , I may be able to recommend one if you let me know where the people are. Try the other things first though

IN a way it's a matter of beinga detective and systematically eliminating posible causes.
Lindsay