Flex always saves data to external files, including fwdata, and the clipboard as NFC (composed) but internally everything is converted to NFD (decomposed). If a person types NFC, pastes NFC, or imports NFC, we still convert it to NFD internally, but then save it out as NFC. Flex does not offer any other options. So when working with Paratext, Paratext should be set to use NFC and everything should work OK between the two. On the question of Interlinear text, it’s always NFD inside of Flex, but I assume in PT everything should be NFC.
The main issues you might run into is if you are using bulk edit options in Flex, your converter needs to handle NFD data. If you are using a Keyman keyboard where context is important, then the Keyman keyboard must handle NFD.
Ken