The proposed urban development zones ( do not represent a new principle; it was employed in "Operation Bootstrap" in Puerto Rico.
(A) stays the same
( B) represent not a new principle, but one that was employed in "Operation Bootstrap" in Puerto Rico.
( C) are not a new principle; the same one
Why is B, right? I think there is contrast and the proposed zones urban zones still exist.
It's actually not important that they still exist - the first part of your question is the key - the contrast.
(A) is wrong because subject/verb agreement is wrong. A plural noun should not be followed by "is."
(B) is a nice use of the "not [x]..., but [y]" construction, and it has proper subject/verb agreement.
(C) also has subject/verb problems. "...are not a new principle" is a plural verb ("are") trying to co-exist with a singular object ("principle").