System Information
Windows 10 version 1607
Blender Version 2.78a

Short description of error
ctrl + Z breaks Boolean link to object that has transform constrain the other way
object A has a boolean difference modifier w/ carve solver applied to it and object B is the cutting object. Now object B has it's location constraint linked back to object A. At any time in the future after any number of operation, pressing ctrl + Z will break the boolean link that A has to B

Exact steps for others to reproduce the error
ctrl_z_boolean_error.blend

Select BooleanCube and apply boolean modifier to it.
Select Difference as the modifier.
Select Carve as the Solver
Choose cutting plane as the object of the boolean operation
Now select the cutting plane and add a location copy constraint.
Choose the BooleanCube as the object of this contraitn
Select the SomeOtherActionCube
Do any number of operation (Delete, Move, Rotate, etc...)
Now press ctrl+z and the Boolean link between the BooleanCube and the cutting plane is broken.