Maybe, but I never would have been faced with this issue as I've been saving new save file on each save to have some back ups in case a quest would cause a save to go corrupt.
The first game I made I had this problem so I decided to go with a 30 saves campaign, I went on a cycle 1 to 30 then back to overwriting save 1 to 30. i nearly made 2 cycles up until last night, so each save hasnt been used more than twice, so my problem is different, it's directly connected to the new module version. When the game says "this save is linked to a different module version" on loading, it works, but if I make a new save after the load, it will crash as the save is now considered "1.0.3 module save". No prompting message, but a game crash on load unfortunately.
It's not a matter of overwriting - every time you save your game after loading (overwrite, save as new, autosave, quicksave - it makes no difference), the "corruption counter" increases by 1 (remember, you have to save your game AFTER LOADING the file to achieve this) . Once this reaches the magic number (35 in 1.0.2 or 45 in 1.0.3), all future saves will be corrupted, and unable to load.
To illustrate, here's an example:
I just started a new game, and the corruption counter is at 0. I save the game to a new file ("save1.sav"). The corruption counter for that save is still 0. I run around for a bit, save to a new file ("save2.sav"). The corruption counter for this save is STILL 0, since i haven't loaded a save yet.
I end up getting caught by Sea Raiders, and reload my latest save ("save2.sav"). NOW, my corruption counter is at 1. I run around for a bit, and save to new file ("save3.sav"). The corruption counter for this save is still 1.
I turn off the game, take a break, and when i load back into the game on my latest save ("save3.sav"), the corruption counter for that save increments to 2. I play for a bit, and save the game to a new file ("save4.sav"). The corruption counter for THAT file is now 2.
Now, at this point I've never overwritten a single file (unless you count autosaves), and I've manually saved a total of 4 times - however the corruption counter is only at 2. Sure, I'll be able to play for a long time - however once this process (load a save, save) repeats 45 times, all future saves on that character WILL LEAD TO GAME CRASH UPON LOADING IN. This is a critical issue, and multiple people (including myself) have sat down and tried to make sense it through testing and looking at the .sav files. I'm sure TW is aware of it, and it will probably (hopefully) be referenced in the 1.0.4 patch notes.
TLDR: Whether you overwrite or save to new file - unless you keep the game running forever without loading, you will eventually reach a point where all future game saves are corrupted, and crash the game upon trying to load. TW is probably working on a fix. Wait for 1.0.4 test result before growing attached to your character.