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,
}
],
}}