The string contact patch on the saddle NEED only be just that, just contacting it. The notch should be angled down towards the tail (just like a nut is) so that it is steeper than the string break angle back to the ball end. In other words, if your string breaks at 15 degrees, the notch should be say 17 degrees or more. But looking at say a stock Fender saddle they are round so have a fairly large patch, maybe 2 mm. How big a patch MAY affect the note? Dunno, but I suspect if it's too big it may.
You say the notch has been filed before, maybe too big of a contact patch, sucking up the vibe of the string. If you choose to refile it I would go with a small 2mm or less contact angled off as I describe. Also make sure to front cut it the same way.
What I would do if I were to file the saddle. Look at the contact area and mark the patch with a sharpie. file angles either direction from there leaving the sharpie mark alone. Also make sure the string sides have a hair of room, just so they aren't touching. I may be crazy tho'. Looking forward to experts telling me so!!
