I'm trying to make a quest that can be failed under certain conditions, and that the player can attempt repeatedly.

However, when the quest fails and is started again, the failed quest will still be in the quest log's inactive section, and for some reason I can't understand, its objective markers will stack with the current (active) quest, so I get two "Go to Location" markers stacked on top of each other. How do I make it so that starting the new quest clears the previous one from the quest log, and also stop the duplicate objective markers?

Not sure how to clear it out of the quest log, but try and add a script that disables your aliases for your objectives when the quest fails then enable them when the quest starts again.

Something like Alias_.Getreference().Disable() and add it to the quest stage that is set when your quest fails.

I have enabled NPCs during a quest than disabled them again when the quest stops as they were only needed to fulfill a certain part of the quest and appears to work fine.

I can't really go around disabling references since a few of my aliases are external and belong to external quests. However I seem to have figured out the source of my duplicate marker problem: I was calling SetObjectiveFailed() in the failure quest stage, and objectives weren't triggering properly due to that. Failing the objectives before calling the failure stage fixed my issue. I still get duplicate entries in the journal log, but I suppose I can live with that.