I've never jacked a trailer under the frame except when it was attached to the truck. That avoids the very scenario you are describing. Raising the trailer by the frame can be very impractical if you're along side the road changing a flat tire. I always use a bottle jack and place it under the spring mount to change a flat tire. YMMV.
As long as you don't get carried away and go very high, I don't think that it will hurt anything, but it is putting a little more stress on the other landing gear. I'm assuming that you're using 2 jacks equally spaced along the frame rails. Using only 1 jack sounds like a bad idea to me.
Howard and Peggy
"Don't Panic"