Removing plating from plated points should be avoided, sure.
Filing points, you are really just looking to remove any tit that may have formed as electricity jumps the gap, taking a few metal molecules along and depositing them on the other point. Maybe you'd file a really bad pitted side, but not often. Replace pitted ones. (one side builds a tit, one has a pit dug 
)
Cleaning with CRC electrical contact cleaner alone should work if the points are smooth and close well but don't make contact. (likely carbon dust and or oil varnish buildup)
Other reasons might be a rusty point rivet, but not on a Lionel I've seen. (Points don't rust easy if at all, but rust dust might foul contact)
