Music imported into iTunes:
> - If you add music files to the iTunes library and organize them within folders on your computer (managed iTunes library), deleting the files from the folder directly may also remove them from iTunes. When iTunes is synced with your iPhone, these deleted files will no longer be present on the device.
Manually added music:
> - If you manually copy music files to a folder outside of iTunes (unmanaged iTunes library), changes made to that folder might not affect the items already added to iTunes unless you take specific actions within iTunes itself. However, any music you remove from iTunes while synced with your iPhone will be deleted from the device during the next sync.
So, if you want to permanently remove music from both iTunes and your iPhone and avoid duplication, it's generally better to delete the files directly from the iTunes library. This can be done by selecting the songs and choosing the "Delete" option from the file menu.