Seems a bit of an odd question.
There are not any shear bolts removed/replaced during an engine change (not on the a/c I work on). Most engines are held in place with cone bolts which are changed (or at least NDT checked) when the new engine is installed.
The shear bolts are part of the pylon installation and won't be touched on an engine change.
I would seriously doubt the integrity of a pylon installation with missing shear bolts, and have been involved in replacing bolts which have become mearly damaged due ground vehicle collisions.