The easiest would be to the original Intrepid files (assuming you have a backup), and alter the specific Warp -lines in notepad or something similar.
Edit: BCUT should have given you a warning, when it could not load the Plugin entirely.
 And incase you don't have a backup of the Ship plugin, here is a copy of the submodel lines from the CGIVoyager, mind you this is from the release a few years back and not from the recent DQ-Pack!
Foundation.ShipDef.CGIVoyager.dTechs = {'SubModel': {
        "Setup":        {
                "Body":                 "CGIVoyager_no_nacelle",
                "NormalModel":          "CGIVoyager",
                "WarpModel":          "CGIVoyager_Warp",
                "Hardpoints":       {
         "Port Warp":  [-0.63, -1.15223, -0.15],
         "Star Warp":  [0.63, -1.15223, -0.15],
                },
                "WarpHardpoints":       {
         "Port Warp":  [-0.6, -1.15223, 0],
         "Star Warp":  [0.6, -1.15223, 0],
                },
        },
                
        "Port Nacelle":     ["CGIVoyager_n_left", {
                "Position":             [-0.32, -1.07, -0.144],
                "Rotation":             [0, 0, 0], # normal Rotation used if not Warp
                "WarpRotation":       [0, -0.45, 0],
                "WarpPosition":       [-0.32, -1.07, -0.144],
                "WarpDuration":       150.0,
                }
        ],
        
        "Starboard Nacelle":     ["CGIVoyager_n_right", {
                "Position":             [0.32, -1.07, -0.144],
                "Rotation":             [0, 0, 0],
                "WarpRotation":       [0, 0.45, 0],
                "WarpPosition":       [0.32, -1.07, -0.144],
                "WarpDuration":       150.0,
                }
        ],
}}