I always thread mine with the presser foot down.
I have never had a problem.
I seldom raise my pressure foot and use the knee lift when sewing. I would take my machine to another dealer, it doesn't have to be a Bernina dealer. I take my Berninas to a Phaff dealer for cleaning/adjustments. I get better service than I did from my Bernina dealer. Plus hes only 12 miles away,
my Bernina dealer was a 30 mile drive.