Admiral, what this does is, after or even before you uninstall all your mods, it will use a repository of original stock game files in a directory called \SH4Pristine to make your game installation perfectly mirror that directory. It will remove any extra files you have and ensure that each file is identical to the original stock file immediately after installation.
Then you can install your mods and be sure you are playing a perfect file installation. In fact, if you have reinstalled mods exactly as you had them before, you can just load up your last save and resume playing as if nothing had ever happened.
As far as the save game files in your \Documents\SH4 directory, SH4CMS doesn't touch that. You are still dependent on your system of backup saves to fix random game save file problems, same as you are for Microsoft Excel. All programs in Windows occasionally save a corrupt file. Whether the problem lies in Windows Explorer, buried in the operating system itself, in Silent Hunter 4, whatever, it's all executable code and not legally modifiable for anyone but the owner of that machine.
Under Windows 10, Microsoft can sample your code, decide it's been altered and delete it from your machine without your consent (actually you've already given them your consent legally although you know nothing about it) and without notifying you before or after their action.
I think you'll find that if your game is completely free from corruption, mod soup, or anything that alters original game files that SH4 will run much better. To that end JSGME is a fault detector, but it can't actually fix the problem once it identifies it. SH4CMS is a guaranteed fix, at the expense of 5.5 GB of hard drive space.
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