When I open a cartesian coordinates file of a crystal structure, I find that Chem3D protonates the structure. Deleting the unwanted protons distorts the structure.
Chem3D's default settings are optimized for people who are *building* structures, so hydrogen rectification is on, as well as the other building preferences. When dealing with crystallographic data, it is not desired for the coordinates to change, and so those options should be disabled. Check for the location of the Building preferences in the manual for your version of Chem3D, and disable them, then open the coordinate file.