Hi Folks!
I'm a neophyte to your system here, so bear with me. I'm doing structural analysis on a timber frame I'd like to build. I have some excellent resource info. but I have a question. When calculating the deflection of a beam (for instance, a summer beam)I understand that structural engineering would conservatively state you should use only the remaining solid cross-section of a beam (actual width less the depth of mortises entering the top face of the timber). Therefore an 8x12 with 2" deep mortises entering from either side of the 8" top face would reduce the cross-sectional area to a 4"x12". This does make sense to me when calculating deflection and bending, but I need some input regarding this idea when calculating tenon shear. I would greatly appreciate some advice.

I assume you are talking about the reduced cross section for a joist tenon in a summer beam pocket. If yes, then the reduced beam (tenon) cross section should be used for shear stress calculations. This is the critical section for shear strengh capacity.