cdaubert:
The Fillet/Chamfer is calculated from the Reference Line of the Beam, which is the Origin in the Profile Editor, but changing this (by moving the Fill relative to the Origin) will not help: the new Beam created when Chamfering will still be the entire Profile, not just the top part you need. Another approach is to convert the Beams to a Morph and edit the Morph, or divide the Profile into two parts: top to chamfer and bottom not chamfered.
You should add a Signature to your Profile (click the Profile button near the top of this page) with your ArchiCAD version and operating system (see mine for an example) for more accurate help in this forum.
David