If you knock her out when she's temp hostile, she will regain conciousness/HP if you rest again, so you may have to do it twice in that case. Sometimes another camp cutscene will superscede the Durge one, pushing it out another night. For example, if you cross bridge to the Goblin camp, or do too many other quests that prompt camp scenes at rest, after you first meet Alfira.
I think Quill was intended as a way to preseve the scene in the event the player kills the whole Grove before that happens, so the knockout thing is totally meta timing. There are ways you can justify it though, like visions of the future or just chaos and happy accidents.
If you rest right away after the knockout that seems to work better. The problem with a temp hostile character for the knockout is that she will do stuff like move around or heal, or call the guards (Lakrissa or Arron etc) so enter TB mode for sure. Sometimes it's easier if you use a control spell like command or hold person to ensure she doesn't push the disapproval too low. You can also use stuff like darkness or disguise self for that.
If you have to do the knockout several times in plain view, and if the faction approval drops too low, this may cause the Tiefs not to speak to you at all during the camp celebration. Silence can also be weird if you fast travel from within the bubble, like not resetting till long rest, I believe it can happen to Alfira as well. This can be frustrating, cause it's not just her but Lakrissa and Zevlor and all the rest too. She'll still be back to normal after it resets before the Last Light Inn, but that takes a few hours to confirm.
The Minthara knockout is very similar, but with the added challenge that if anyone hits a wardrum she won't disappear with the Zhents when the Goblin camp goes aggro, and instead she gets executed at Moonrise before you arrive. I think if you take all her gear that may also result in her not surviving till the Moonrise rescue.
I've attempted this thing with Alfira on several runs as Durge, if you want to see how it works out, there are a bunch of screens and my many rambling missives about it at TavernRPG... It's pretty tough to pull off some of these scenes, and to thread the needle there without knowing in advance what will happen, so I tried to take some notes for myself hehe. Second run journal starts maybe midway down the second page in that thread I think.
https://tavernrpg.com/threads/bg3-honour-mode-strategy-tactics-many-spoilers.388/Best of luck!
