i deleted the file manually. So then i reinstalled it now it says theres missing files
Well, that's quite different from the previous "I didn't removed anything"...that's exactly what it supposed to happen.
Now, it's difficult to say if your scenery.cfg is in a clean state or not. However, as I've said in my first reply, to fix that message, you should go into the Scenery Library in FSX, and manually remove the orphaned area.
Then, it's best if you UNINSTALL JFK first (AFTER you removed the orphaned area), then REINSTALL it.