I think there may be a little misunderstanding in which topics appear in unread. I would explain it as “topics you are tracking or watching that have unread replies”.
Maybe the problem is that the notification level of the topic didn’t change before you marked it as unread. Maybe you can try changing that in the notification dropdown on the topic before you mark it as unread. (It may also be helpful to reload the site after you marked something as unread. Sometimes I have the impression Discourse needs that to show the topic again.) For me, the topic is back in new after that.
If that works it might make sense to change your tracking preferences, for example, to track topics as soon as you enter them. Then you don’t need to do that every single time you enter a topic you want to read later.