[Pisces]

You may have luck by reverting to older saves. Sometimes the cause of the bug happened at an earlier event in the game. Like saving when you are not aware that there were contacts outside of visual range. (To be sure, do a hydrophone check before saving by listening yourself. Then you can be sure nothing is within 34 km radius) Loosing a savegame is less of a loss than the entire patrol. If you go on a long patrol, make sure you make unique saves.

Did you change mods along the course of this patrol? If you did, there might be a conflict with the savegame. Either restore the mod order and hope the savegames start working again, or just begin a new carreer based on the mod status quo. As a rule, never make changes to the game while in a patrol! Some pure graphical file changes might be an exception.

Also, for SH3 Commander. Make sure it is not installed in the default location in Program Files. Commander makes backupfiles of the changes and stores this in it's root folder. Windows does not like it if programs change files in the protected Program Files folder and reverts those file changes. Installing it elsewere (like C:\Games\SH3Commander) avoids those issues.

SH3 Commander also has the rollback function. Can you provide more information on what it shows before you start the game from SH3 Commander? I'm a bit rusty on how to restore synchronisation between it and the game but it may give others a clue.