You need a tune to disable the factory bypass valves or else your car will go into limp mode and you'll be limited to wastegate spring pressure. Some vehicles only require to have one plugged in, other strategies require both. I'd recommend zip tying them in place, do a datalog, then unplug one, datalog again, and compare boost. If your boost level doesn't change, you can remove that one. If it limits to 3-7 psi, plug that one back in and unplug the other and log again. If this allows you to reach full boost, you can remove that one and leave the other plugged in.
Ortiz Performance does offer the ability to remove the factory bypass valves in our tunes, but similarly to the above not all pcm strategies accept the changes. On some SHOs the switch is inversed and we have to change a few different things to get it to work, and in other strategies the switch doesn't work at all. SCT has deemed the SHO a dead platform and they are not interested in making any new changes to the tune capabilities which is unfortunate, but we do have R&D level access which allows us back end capabilities to try additional changes which can occasionally get it to function properly, but often times it is easier just to leave them zip tied and hidden.
