What is changed
Left out: every code type, value and UDF you don't tick, plus every place it's used (activity, project and resource code assignments, UDF values). A kept value always keeps its parent values, so the code tree stays whole.
Kept exactly as exported: everything else - activities, relationships, calendars, resources, assignments, the project and its settings. Kept lines are copied byte for byte, in the file's own encoding.
P6 never deletes anything on import: leaving a code out only stops it from being added. Your picks are remembered in this browser by name, so next week's update can use the same ones (Use my last picks).