Getting stuck in the open ocean without any chance of getting the engines restarted has happened so often to me ...I religiously keep separate unique saves all throughout each patrol.
Plus... doing this also thwarts that
"saved game refuses to reload because the file has been overwritten too many times" demon.
If it were possible to alter the files you asked about ...and I knew which ones they were I would tell you...but alas I don't....and I would be doing it myself when the need arises.
Lets hope it is possible and that somebody knows and will tell so we can both benefit.