You probably ought to note which version of firmware it has on now (info from app) and ask on the Phantom 3 forum here.
http://www.phantompilots.com/forums/pro-adv-discussion.81/ 

I do vaguely recall some problems of linking being lost if done in wrong order, or not not doing an intermediate stage.
Probably not something that can't be resolved if you do feel brave enough to just dive in.
The controller can be updated separately from a memory stick rather than the card in the Phantom slot.
I'd be surprised if all was not well just pushed straight to latest version especialy when you have the latest app apparently working with it (?)

I found this reference to an encryption change causing probems.
http://www.phantompilots.com/threads/rc-firmware-update-1-6-0-to-1-8-0-failed.93166/#post-964830