The paper does not specify how to generate those efficiently, and I haven't given it any thought yet. I don't know of any implementations of the paper, but this aspect of it should be common enough.
EDIT: sorry, didn't read your comment fully. I'm not sure what you mean with "all permutations of possible deletions". The d-deletion-Neighbourhood of w contains all sub-words of w that you obtain by deleting any d letters from w. For d=2, take any two letters and remove them. N₂(jamra) = {jam,jar,amr,jaa,ama,jmr,jra,ara,mra} (hope I didn't forget any...)
Does that make it clearer?