I'm not sure if this is a stupid question, but is it allowed to fix bugs and deploy a new version? I guess no.

I saw that others have added new versions. Is it okay to add another version and replace the web version, as long as the original windows version still exists? Or do I need to keep the original web version?

You can upload bug fixes, just keep the original 7DRL version accessible somewhere for jurors and for people who is curious about what is possible in 7 days, and make sure to state in your page (and in-game) that it is an updated 7drl++ version or similar.