Was sure of that 
You can try the last deconz version 2.20.x branch if you can ? nothing concerning your issue, but some improvements.
You can’t make the try on another hardware for somes days ? you can make a clone of your zigbee network using phoscon restore/backup option ? To check if the problem come from the gateway.
Always the latest 
I don’t know if I can try on Windows; My wife could kill me. 
Computer isn’t in an optimal position so that the coordinator will not reach many devices that need direct link to work properly.
You have device that need direct link ?
But yes right, if there is too much placement difference, some devices like aqara/Xiaomi can disconnect.
I don’t know linux enought to check if the problem is from the USB port, the gateway, the OS or deconz using linux log but have you make a try with a powered HUB ?
