I'm at work now, so I can't remeber the exact file structure, but there are .MIS files for each of these new mission types in SH4. They are stored in folders called 'PatrolHonshu01'or 'PatrolCelebes04' or something like that, under another couple of folders I can't remeber the names of.
Anyway, these .MIS files reveal the length of time required to complete the patrol. Unfortunately they give a numeric value, with no measrement. The default I believe is 2880. I couldn't tell you if it's hours, minutes, seconds, epochs or whatever. but if it's minutes, that's 48 hours. And it could vary from one patrol to the next, I haven't looked at them all.
The bottom line is that you will eventually complete the objective. I would suggest running submerged during the day, and surfaced at night.
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