I have had some corrupted save files too in the past (mostly because of saving with bugged objects nearby - usually a result of me modding files that shouldn't be edited
).
To counter this problem I always save into a number of files.
That is, the 1st save of a patrol is called "1", the 2nd "2" and so on until 4 / 5 saves, after which i start at "1" again.
Now in the rare occasion a save is corrupted I load the previous one, which generally works 'cause there were other objects near the sub when I made that save. This way I never lose more than something like 15 minutes.