Exactly, KaleunMarco... and "yes", the existence of a "bugged" Save can seemingly (though not always) influence the other Saves.
For whatever reason, the devs seemingly did not put any error checking into the Save routines. other than maybe MS dll stuff from the WinXP days. They do have one file in each of the Save folders that is a "counter" (file size), if you will, and that appears to be the only "check". The last Save will usually be written to two folders, but that appears to be it, as far as "integrity" goes, and whatever the game does while it writes the files. It seems that one little "hiccup" in the process will bonk the whole Save, yet not tell you about it. You find out when you go to re-load, what you thought was a Saved game. "Bad" data can include anything from a mod gone wrong, to an error in a ship config (which there are a few in the Stock game), to any one of a number of scenarios. This is NOT to say that most Saves are bad. Most are good, and definitely at a higher success rate than SH3 - but there is no consistency here.
A really odd thing can happen though, if you have a bad Save, and that is that if you go back to a previous Save and it loads, then go back to the Load menu and try the "bad" Save again, it will sometimes load fine. Absolutely no idea why that works. Someone just a couple of weeks ago mentioned loading the "Leaving Port", then stepped through all of the "bad" Saves (four of them??), and had success loading a Save that wouldn't load previously. Very strange.
As far as the Save process itself goes, you are better off saving while surfaced (not 100% necessary, and sometimes not possible). If you are submerged and have to Save, do so above the 500 foot depth. Below that, and your boat does not always come back up. Nothing like loading a Saved game, only to find that your sub is sinking, and won't stop going down... Try to Save when it is relatively quite. Let audio files finish playing, don't be on the sonar screen, etc. The simpler the screen displaying, the better. I will try to Save while on the NavMap with as little activity as possible showing, or on the Attack Map, Periscope screen, etc. Something that is not 3D. Again, this is not 100% necessary, and does not guarantee any semblence of success as far as I know. Not Saving too close to Land might help also (what, after all, is "too close"??). Don't have any ordnance enroute, and it is usually best to not have any repairs to boat damage outstanding, except that which cannot be repaired. Several aspects of the game run on "timers", and as such will re-set with a Save ("weather" is another). As an example, say the repair screen says it will take four hours to repair a leak in a compartment, and you Save at 3 hour and 52 minutes, with 8 minutes left in the process. When you reload that Save, you will have four hours and zero minutes to wait for the repair to be completed, not the 8 minutes that you expected. If you gotta leave the house though, say to pick-up the wife after work, you do whatcha gotta do
and expect to have the fours repair left to go on the re-load...
Probably the biggest thing, is do not overwrite a previous Save. ie: You leave port and Save the game with "3rdPatrol Tambor", or whatever. You encounter a Convoy, and Save the game prior to the attack, but use that same name "3rdPatrol Tambor", that would be an overwrite. Instead, use something like "3rdPatrolTambor01", "3rdPatrolTambor02", etc. That's another thing some of us do - no spaces in the names, though again, not 100% necessary, if at all... lol - I will also usually pause for about 10-30 seconds after Saving, and try to make certain the file is finished being written. Another thing is to NOT save the replay, unless you are Saving a SingleMission or WarPatrol for use as a "video". Saving the replay will result in a ~huge~ Save file, increasing the chance of an error, which will compound over time, sort of like mortgage interest ...
A lot of these points are leftovers from the SH3 days, and some folks ~never~ have a bit of trouble with Saves. Go figure...
