jnshmoo, Markus did pop into one of the threads about post-deadline trades initiated by the AI not needing waivers, but we haven't heard anything like "Gee, I guess this update needs a patch".
ctorg, Just did a roster export / import, and the players were all in DFA... but when I ran Computer Manager (either team by team or the "all teams" button under League Setup), all but a handful of players went to rosters, with 4-7 remaining in DFA. Nobody disappeared. *shrug*
If you can make it happen again, I'd be curious to know if the disappeared players are in the draft pool.