No, the choices during her events don't prevent you from seeing later events.
Did you check the walkthrough? It has a step-by-step for the event lines of all main characters.
"Character events sequence:
1. Catch her while changing when entering her room with 30+ relationship.
2. The quest "Magic License" start with 45+ relationship. You might need to talk with her two or three times before you get the dialog.
3. When you're at the point of the main story where you have to search for Frall in Amagal, you can talk with Chiyo for the "Varea" quest. If you meet Varea and Frall before talking to Chiyo the quest and dialog is skipped.
4. When entering her room with Kayelinth's playlust over 80 and previous scene. (Chiyo and Kay playing in the river CG)
5. Talk with Chiyo with 70+ relationship for her masturbation scene.
6. Her “alchemy” events start when you had the introduction dialog about alchemy tables (all blacksmith with an alchemy table trigger the dialog) and the festival of Thremten done. The second step requires the mithril pickaxe, which you get during the main story events. (Kissing CGs)
7. Talk with Chiyo when the main story is at it's current end (Varea in your Castle) and you've met King Merius of Amagal. King Merius can be found when going to the Yang Tower and fixing the magical circle in the cellar. The circle requires that Chiyo's magical knowledge is at 50+ to repair it.
8. Talk with Chiyo again for her second masturbation scene.
9. The next step requires that Chiyo is level 25+ and that you have constructed the big farm on the country overview map. (The farm where you can release monstergirls) The dialog will give you the "Gold License" quest.
10. First sex scene is available when talking with Chiyo after the gold license test."