Network Topology - Parent-Child Relationship Lost

I've used the ZDO_IEEE_ADDR_RSP to generate the topology of the network.  It has worked fine, but I'm finding that after the network is running for several weeks (nodes leaving network and rejoining) that the discovery ends early.  The children of a node are not appearing in the AssocDevList.  I rewrote the routine to pull the short address from the database to pass to ZDO_IEEE_ADDR_REQ, rather than from the parents AssocDevList.  This allowed me to get a complete picture of the network, but its broken up into 7 or 8 mini-graphs.  Is there away to avoid the loss of the parent-child relationship?  Also is there a way to recover this information?

Also, I'm seeing some nodes have two or three parents?  Any suggestions for fixing this?

Thanks!