Oh... I don't like Tokko in Bleiente's version anyway... I die ~way~ too soon...
So you're probably fine with the mods, and you've just experienced one of those "unknown" situations with your save game. I saved the game years ago just after a very intense depth charging where they broke my batteries, and I had to surface, since I'd lost most of my propulsion, ~and~ the boat was filling with poison gas. Once on the surface, I was in fog and it was raining. I saved the game and came back the next day. When I loaded the save, the skies were perfectly clear, and the DD's that had given me a depth charged drubbing, now gave me an intense 5" shell pounding... I died... I'm thinking that was v1.4 way back when.
Like kimuraijn suggests, when saving, name your save, and don't overwrite previous saves, and that minimizes the chances of encountering those issues. Some folks never have issues, while others have never-ending troubles. The computer's and game's settings probably come into play some. Activating mods, and then loading saves from before the mod can do what I call "cross-contaminate" your game, and you may never know it happened until you have this bad "restore" issue.