Everything is back to normal now.
I reverted the version back to 3.4.1, which didn’t work. I then killed off all containers on the server, which did not work as well. I also killed off port 80 on the server, but still didn’t work.
In the end I found out it was also because I installed bcrypt due to the annoying warnings on meteor start, which led to meteor not starting up on the server for some reason.
After removing bcrypt, I was able to deploy successfully again, and my database was also intact.
Thanks a lot for the suggestions.