I tried deleting it and it decided to delete my entire download folder

It deleted my download folder when I tried to unistall

In order for us to provide better support, we need to see the log generated by citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File

The installer clearly warns you about that when you create a custom installation location. It tells you that everything in the folder where Citra is kept will be wiped when you uninstall. It even tells you this in the uninstaller, right before you uninstall. We’re not responsible for you clicking through things without reading anything.

If there was something important in that folder, you can try recovering it with something like recuva.