Yes, it is just the Nick building and not Jimmy Neutron or anything although the small Nick store closed also. Nick made a contract with Universal in early 90's . Newer contracts were related to characters and Jimmy Neutron the ride and they are not effected.
The other contracts are much newer and do not include the building since it had a different contract. That simply means that the new contracts will allow Universal full access to characters, Jimmy Neutron, and Nick merchandise.
It was a business decision. I don't know if Nick decided not to extend or Universal made the decision. Nick is owned by CBS and Universal is owned by NBC. Maybe Nick just decided to put all their energy and shows into the new Nick Hotel that is just opening up in Orlando.
Anyway, it is just like Disney breaking ties with MGM, strictly business.