This is a pretty good question, one that’s been on my mind recently. I do a lot of organization, and figuring out what to note and what to leave unnoted is essential for sanity. Great ideas often come when you are incapable of writing them down, and even when you’re not incapable, it’s often highly inconvenient. Suddenly grabbing your notebook while you’re deep in trance will knock you out of it and you might not have the motivation to restart it.
Ultimately I think the answer is to just remember them and write them down later. If it’s a good enough idea, you won’t even have to remember it, your mind will bring it back up to you later when you can write it down. We often underestimate the capability of our subconscious minds to do this sort of thing for us.
Also I never sweat a missed opportunity due to not remembering an idea. The reality is that ideas are plentiful, while energy and time are the limiting factors. You’ll always have more ideas than can be executed on.