I'm pretty sure Bend Tech will do that automagically as long as you do the cutting within Bend Tech prior to generating the cut/bend instructions. You can check for yourself by putting the assembly together without cuts, check the bend/cut length instructions, then add the cuts/notching, and recheck the instructions to be sure the cut lengths were adjusted.
Also the notch wrappers are based on the inside or outside intersecting surfaces (depending on which side of the cut you're looking at), so using the right material thickness in your assembly is important.
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