Neves was certainly heavily involved in the McCann case. It was he and Encarnacao who met with the McCanns to update them, not Amaral. It was he and Encarnacao who allegedly interviewed them on 8th August and asked questions which should have been asked only of aguidos. It was him who Bob Small phoned when the McCanns were panicking about being made arguidos. When questioned at Amaral's trial, however, he played down his role;
The Judge asks the witness if he intervened in the criminal process related to Madeleine McCann's disappearance.
LN says he did, but not directly.
The Judge – What do you mean by "indirectly"?
LN says that, though he went to the Algarve a few times to meet Guilhermino Encarnação, then Director of the PJ in Faro, and Gonçalo Amaral, the operations were performed by Portimão police officers under the direction of his team.
http://miscarriageofjustice.co/index.php?topic=2600.0Amaral, however, makes it clear in his book. A team from the DCCB came from Lisbon with their director (Neves).
From then on, two deputy national directors (Neves and Encarnacao) would direct the investigation assisted by the coordinator (him).
I think the same thing happened in the Cipriano case too.
