Is cotton thread harmful?

We took a little class on the Brother PE 770 last Monday. Immediately after that, we came down with the worst case of flu/allergy/cold in world's history; haven't felt like seeing what/if we learned anything. However (!) I do remember the Brother lady saying that cotton thread on the upper would cause eventual damage to the emb. machine and that would be very expensive to undo. It was a great class and a wonderful shop; we'll hope to go back many times. I do wish we had asked further about the 'no cotton' warning. Do you imagine that was just 'her' shop's experience with cotton? or a 'real' Brother proclamation? Any thoughts? Polly