Yes, that is the right way.
The fault is the D: disk (the saves), as you suspect, but not for the same reasons.
The D: disk works as a removable disk, each game has its own disk.
If game 3 is installed, disk D: of game 3 is created.
If you close and open game 1, obviously the D: disk is different, it is from game 1.
When a game is installed, the registry is modified, where the links go, the disk path and other things.
If you close and open another game, Windows sometimes does a quick registry check of the newly installed game. If it gets that the paths are not the same because it is another hard disk, it will do a scandisk. This is random and I have no idea why it happens.
I already discovered it, there are games that install only the game files, others install some component in the Windows directories, these are going to be verified in the next reboot.
To avoid this, the ideal is to always reboot after installing a game. Although this does not prevent a system crash or if it closes badly.
To correct the problem the escandisk warning:
Start PURE and from the menu start Windows, without loading any game.
When finished restart Windows from the Start button.
When the reboot is finished, shut down normally as you do.
At this point I am going to recommend you to freeze the disk. It is a little uncomfortable at first, but very useful because the C: disk is not modified and is not damaged.
In the ‘OS Disk Modifications’ options there are 3 options.
‘Keep’ is normal, ‘Discard’ freezes the C: disk and ‘Save Difference Per Core’ is a new and wonderful option. In the description it explains what they are for, I am going to comment you how to use ‘Discard’ well.
Before closing the core, activate ‘Discard’ and the disk freezes, nothing can be installed.
If you want to install a new game, before starting Windows you have to put the option ‘Keep’.
You install the game, restart and close Windows. In the screen of it is safe to close, you activate ‘Discard’ again.
Now you can close the core whenever you want, you don’t have to shut down Windows, it will never get damaged. @thingsiplay This may be useful for you.
But Windows 98 doesn’t have official SP1, it’s a hack, I never got to approve it, I have no idea if it’s any good.