As I said elsewhere, the bond works both ways, and I highly doubt Egwene is going to accept her actions being tracked as a cost for tracking Rand's.

And I'm really not seeing any way that Egwene would demand this bond in secret. It goes totally against her views on this issue, and the way she looks at how she must deal with Rand.

On the other hand, one way this may happen is if she and Rand decide its needed for them to be bonded so that once Rand executes his fake death plan, Egwene would be in the know as to his location. I doubt it, because the fake death itself is something I'm beginning to doubt, but its a possibility.