I have always used Minwax or similar polyurethane brushed on from a can, using a foam brush. Never actually brush loose paint - only let the urethane drip over the damaged area from 1/4" above the surface. It will self level and cover with minimum disruption to the paint flakes.
Never had any problems with ink dissolving, damage to the glass, or sheets of paint coming off down the road. Been doing it for more than 20 years now with zero bad effects.