Hi,
I think that in your case there are no problems with the network.
The inherent property of ZigBee network is to route data between a source and a sink automatically. This means the network 'data' topology (from the data traveling point of view) changes from time to time due to the changes of external conditions. Given the wireless nature of ZigBee solution one can expect that this topology will change quite often.
Subject to the network consisting of the routers only, the parent-child relationship doesn't matter for the data routing. So the 'parent-child-based topology' doesn't reflect current routes and corresponds to the moment of the network formation. As times goes by, both the short addresses and the parent-child relationships can change and to get the connected graph one need to be sure that these changes don't happen during the topology discovery procedure and that the corresponding information about every node is updated.
Regards,
Ilya