Any engine I've rebuilt, and most factory manuals you read, always recondition the rods and replace the rod bolts, Pretty much standard fare in reconditioning/rebuilding an engine.
I usually in most cases replace all bolts the are involved in the areas of suspect. Head Bolts and/or studs and nuts, clutch, flywheel, etc.
I would think on a diesel with it's much higher compression that head bolts would be given. Are far as in your case, was the Rod still attached to the Crank? Or did it fail at the bolts? The comment about 2 or 3 bolts turning easily the last 90 degrees, should have been a tip off. I'm wondering at what Torque were they last tight?
You did bring the Torque up 5-10 lbs at a time before the final once around to finish?
What type of torque Wrench were you using? Click, Bar or Dial Indicator type?
71 250 Coupe
92 400E Sedan
90 944/S2 Cabriolet