i chopped down the flat bar on both my folder and my hybrid after i came to the conclusion that wide bars are uncomfortable for me. in both cases i took ~2" off each side. on my dahon folder i went from 23.5" down to 20", and on my hybrid i went from 25" down to 21". both times i just went to my local bike co-op and used a hack-saw with a special jig to make straight, even cuts, and then filed down the burrs. pretty straight-forward and easy. those changes might sound small, just a couple inches here or there, but it makes a very noticeable difference.

i am very pleased with the results, i don't know why your LBS would recommend against it.