S3D doesn't do auto-updates like that. You would have had to go to the S3D website, download the software installer, run it, and then even then the new version is always placed in a separate folder (for example C:\Program Files\Simplify3D-3.1.1 vs C:\Program Files\Simplify3D-4.0.0). So I'm pretty sure you would have remembered if you followed all those steps
Now a prompt that I have seen is a profile update, for example, when they updated the settings for my FlashForge Dreamer. It alerted me that there was a profile update, but you still had to manually select that you wanted to download the new profile. It wasn't automatic, you had to choose "Yes" from the prompt when it asked if you wanted to download it. So maybe that's what you saw.
If you want to turn that off, just choose No when it asks if you want to download the new profile update. It won't prompt you again after that.