I'm not sure if I'm understanding the problem correctly, but it sounds like the problem might be that you've failed to rename the save file correctly?
If that's it. It should be fairly easy to rename.
Let's take what you have for an example:
You've got save Slot_00000003.save.ver1. What you would do with this, is rename it. Slot_00000003.save to be able to see it in-game correctly.
It doesn't matter what numbers you give your saves. If you want to take them back into game, you'll need to take the .ver1 off the name.
Take a look at the link below for more on restoring saved games.
How-To: Restore a Saved Game
http://www.carls-sims-4-guide.com/forum/index.php?topic=21519.msg387147#msg387147