In most siting scenarios, it is reasonable to assume that the submerged horizontal acceleration section can be protected from external hazards simply by placing it deep enough underwater that ships can pass overhead without risk of impact, and by maintaining a well-patrolled exclusion zone that prevents fishing vessels, trawl nets, or dropped anchors from coming near it. Such measures greatly reduce the probability of external damage. However, to maximize the number of viable sites for the system, it is useful to consider locations where these protective measures may be insufficient or cost-prohibitive, and to allow for the possibility of minor but occasional damage to the submerged tube. A second motivation is economic: it may be more cost-effective to engineer in tolerance of occasional spinning screw segment failures than to design every screw to be completely failure-proof. Therefore, although uninterrupted operation without damage is preferred, the ability to isolate damaged sections enhances both feasibility and economic performance and is worth examining.

In both failure scenarios, the system must be able to isolate a damaged section quickly enough to avoid catastrophic loss of vacuum to the entire system and isolate flood damage to the affected section.

The submerged tube is built as a concentric double-tube assembly consisting of a heavy, pressure-resisting outer tube (for example, concrete) and a higher-precision inner tube that maintains the vacuum. Mechanical actuators between the two tubes allow the inner tube's position relative to the outer tube to be dynamically adjusted to achieve a high degree of inner tube straightness. The annular space between the tubes is large enough for inspection robots and repair robots to travel, allowing continuous monitoring for leaks or corrosion, and enabling robots to make minor repairs such as applying fresh paint or patches.

Acoustic and vibration sensors on both tubes will detect either external damage to the outer tube or internal damage to the inner tube, determine if the damage is sever enough to warrants isolation, and if so, which section to isolate.

At each section boundary, there is an evacuated compartment that contains a circular isolation plate that can be slid between the sections and then affixed to the tube to isolate the sections from each other. Before this can happen, the sections must be mechanically separated from each other using hydraulic pistons by a distance roughly equivalent to the thickness of the isolation plate. At section boundaries, the screws will need a double bracket so that act of separating two sections doesn't leave the screw segments at the end in one of the sections unsupported. The act of separating sections at the section boundaries will compress some of the undamaged tube upstream and downstream of the section being isolated. This compression will be absorbed by slack between screw segments and by expansion pleats spaced periodically along the inner vacuum tube. As soon as the isolation seals are made, compressed air will be released into the damaged section to help mitigate a water-hammer effect that might occur, in the case of extreme damage, if water rushes in rapidly.

Once the damaged section is isolated, a repair barge can be deployed to the site to effect repairs, or potentially replace the entire damaged section.