So how this reads to me:
TOR has uninstalled itself, including its Repo Key. What it hasnt done is remove itself from your software sources list. So your update program tries to query all of its repos, and finds it cant talk to the torproject.org repo anymore, so it dies a horrible death.
Check your Software Sources (it should be in your menu) and remove the TorProject repo from them?
EDIT: Or, if you still need to get packages from the TorProject repo, go and get the PPA key for that repo again.
But if you check the versions for each item itself there will be different versions for each one. The packet manager will pick the applicable latest for each and force that.
Then the it will write a new current list of updates for the Update Manager.
I can’t remember if the “could not refresh the list” error was ever experienced when updating through the package manager. Maybe it’s a shortcoming in the Mint Update Manager if it can’t handle packages marked upgradable in the package manager.
Mind though, I’m really not sure this quick fix would have fixed your original issue. It’s what I usually first try when the Upgrade Manager throws an error like that.