Your problems with stability seems to be in the realm of the Zigbee network and not an issue with deCONZ or how you run it.
Make sure you threat the Conbee stick as a radio transceiver with an antenna which is what it is. Place it where it gets good radio coverage and on a 1 meter USB extension wire away from noisy computers
And you may very well have a device in your network which is a shitty router. I did not get stable network until I got rid of all my Osram smart plugs or rather dumb-plugs and replaced them with Philips Hue equivalents. There are just mains powered devices on the market with crappy routing software
See this debugging topic I wrote a while back