Just in case other people needs to manually unstage a user:
Step 0: SSH to your VM
ssh my.discourse.domain.com
Step 1: Enter the discourse container
cd /var/discourse
sudo ./launcher enter app
Step 2: Enter the Rails console
rails c
Step 3, Option 1: Unstage the user by email address
User.find_by_email("email@address.com").update(staged: false)
Step 3, Option 2: Unstage the user by username
User.where(username: "username").update_all(staged: false)
Step 4: Finito, get out
Press ^D a few times to get back out.