That's what I'm getting at. You can cross-contaminate the Saved Game and the new Game configuration if you use old Saves.
Say you're playing the Stock game, no mods. You have a great career going, and you've Saved a replay of one of your Quick Missions that you're going to go back in and playback and record to a movie with MSI Afterburner and then convert and post it on YouTube. You'll be famous. If you add a mod, say Trigger Maru Overhauled v2.5 while doing all of that, and you load that Saved Game from the Stock version into the new TMO version, you stand a chance of ruining your TMO install and the stock Saved Games you have. Same thing happens in reverse, if you save data from a TMO career, and then remove the mod, you can no longer use the TMO Saved Games. That all comes about from "compatibility", or lack thereof. Changes are made to the game with the mods, rendering old Saved Games incompatible, and as I mentioned, you can ruin a good save by loading it in an incorrectly configured game. You'd think the game would have something to catch that for you, but it doesn't.
The Save folder is limited to a three character name by the game, hence the "SH4" name in My Documents. MultiSH hooks into the filemanager.dll of the game, and let's you change that. So for my mods, I've got SH4 is a "Stock game Save folder", FRS is a Fall of the Rising Sun Save folder, TMO is for TMO, FSU for Fall of the Rising Sun Ultimate (etc.). You can use MultiSH4 to help you have several installs of SH4, and a different Save folder for each of them, or you can use it to swap Save folders in and out for you - although I always got confused doing that - "Let's see, what is my Save folder?..."
As you experiment with mods, you could also copy and move the folders underneath the SH4 folder, and then let the game create new ones for the mod you're using. Get finished with the mod, you can copy that data folder and move it elsewhere, if so desired, and then move the old Saves back in the SH4 folder. The only problem with changing those Save folders is that you do lose the screen settings and gameplay options you set previously
