After putting all the glass parts on the colourful mirror in the church, return to the Library 2nd floor where you found the chest with Greek password. Then Koudelka would open the chest and get Sophia's Letters. When you face Charlotte and give it to her, she remains the Flare Brooch.
These secret items are on a time release. You\'ll only be able to get them once during each adventure. To activate the release, you must have a certain number of items in your inventory. If you have 10, 21, 32 or 43 items in your inventory at the following times, the corresponding secret item will be released.