To summarize what the others have said, this is the infamous "submerged save" bug left over in the code from SH3. It is hard coded in the engine and has nothing to do with TMO or any other mod. The 100% damage bug can happen to any save regardless of depth. Never save the game submerged. It is too risky and the chances of broken saves and broken careers are rather high. Depending on how many saves you have, you may have no choice but to abandon the patrol or career because there is no resolution to this bug.
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