The only damage that I've ever read about re: over-brushing has been enamel damage caused by abrasives in toothpaste. The bristles of the brush should be much softer than enamel.
I had this problem for ages, in the end, the actual problem was gastrits. Any gastric problem has that same simptom, so if it persists, go check for them.
I don't doubt you, but that might also have been advice for after the filling perhaps? The stuff they fill it with is not nearly as hard as the stuff on the outside of your teeth (which is pretty damn hard). So a filling will always be a weak spot.