And just to be clear, partially solved puzzles are not saved to the original files. The original .puz file never gets modified. Instead, a partially solved puzzle is saved to a special binary file in the "/home/user/.crossword_puzzles" directory. Basically, just your answers are saved.
As stated on the bugs section of the project page, xword can't deal with "locked" puzzles. I don't know the encryption method for those puzzles and thus I can't write a decoding routine. Sorry.