One thing about the game, and it is a bugger, is the Save system. SH4 has the same basic "Save" system as SH3. One of the big differences is the size of the campaign. SH3 has the campaign inside of three ~HUGE~ files. EVERYTHING about the world is contained in those three files, so the data there in the Campaign folder is what loads any time the game is run. SH4 has the campaign split not only into different functions/areas and different time periods, but it also loads the 3D world "dynamically", only as the player gets within the "spawn distance", whatever that might actually be - but it is beyond the horizon...
Anyway, the similarity is that if something has occurred in the game, and the whole "incident", whatever it might be, hasn't "cleared" from the game, then you will repeat ad infinitum ad nauseum those certain aspects of the game. If something that is broken in the game from the original programming, and you happen to encounter it, such as the anti-subnet sound (it is horrendous), then every time you restart the game, you will encounter that incident. With the anti-subnet sound, every time you re-start the game with a Save associated with that sound, you will "hear" that "ScKreeEE!". Yeesh! Your boat might also take damage again.
Similarly, if your submarine has taken damage, and you Save the game afterwards without the "repairs" being completed, the "clock" for the repairs restarts again. So let's say you have control room flooding from bulkhead damage. It is going to take 2 hours and 30 minutes for complete repairs (just an example - not a real figure). You have to get to work in real life though, and only two hours of game time has passed since taking damage. You still have 30 minutes of repair time yet to go. But you've got to leave for work, so you Save the game. After you get back home and load the Save, your damage is back to taking 2 hours and 30 minutes to complete. Plus, you oftentimes get the "sounds" associated with that damage as the game loads. Really strange, and disconcerting sometimes.
KaleunMarco might not be encountering that though. I can't find anything obvious (besides the fact that I am not sure of what I am looking at, much less for), but it might be that in an attempt to make something difficult to repair in the mod, it is getting stuck in a cycle instead. Just a guess though. Maybe if KaleunMarco can let us know if a re-start of the game and/or computer eliminates the damage cycle?