Should I stop meditating to note a thought, or let it go and stay in the session?

This is a genuine dilemma, and you do not have to choose between losing the thought and breaking your practice. Usually the best move is to gently let the thought pass and trust that the important ones tend to return, keeping your attention on the session. If it feels too valuable to risk forgetting, a very brief note is fine. The trick is to capture it without fully pulling yourself out. StillMind makes this easy with quick voice notes, so if something really matters you can save it in a few seconds and settle straight back in, rather than getting up and hunting for a notebook.