How does Restore Defaults command affect performance of the XBee Zigbee module?

I am using XBee Zigbee SMT S2C module with firmware 0x405F acting as ZC for one integration project acting with 3rd party device acting as ZED. I observe some issues during association: sometimes ZED just doesn’t try to join, even though there are Beacon Request and Beacon packets present (captured with RF sniffer). Network reset with ATNR command doesn’t help much. However, if I do reset of the ZC to default settings with ATRE command and configuring with the same settings as before, ZED might join the network.
I am wondering, what effect Restore Defaults command has on the module performance, if any.