Sometimes you will find that blocks become unjoined when you make a cut in 3DEC. This is because joined blocks must make a contiguous volume. See figure below. Imagine 3 joined blocks. You wish to create a true joint through the left block. The right block will be cut as well since you can’t have a joined volume with cuts going only part way through.
The way to deal with this is to make sure that you set the unwanted joints to be elastic with large stiffnesses so they have minimal effect on the results.