Put your project under source control if you have not already, or otherwise completely and totally back it up before trying anything more.
Once you have done so, try closing Unity and deleting the Packages directory and reopening Unity, see what it wants to install.
When you are using source control it’s trivial to back out of attempted upgrades like this. Personally I use git because it is free and there are tons of tutorials out there to help you set it up.
Here’s how I use git in one of my games, Jetpack Kurt:
Using fine-grained source control as you work to refine your engineering: