Recently I discovered that when I go to host shutdown in HA, next time I turn on the system all entities from conbee 2 are unavailable in the system. This is fixed by restarting HA and once restarted they show again. The whole time though they are visible in conbee 2 (phoscon for example).
Have you waited long enough to see if they back online on their own? for me it often takes a few minutes, could be longer for battery operated devices. I suspect the Conbee is waiting for them to send their state to Deconz. You mention you can see tem in Phoscon, are they grey there or black?
I have another experience by the way, for which I reported a bug - If I restart HA (with lots of integrations) the deconz integration isn’t fully up and running yet when the automations get loaded. This results in triggers for buttons not being activated. I worked around this for now with an automation to reload the automations a minute after startup.
I have waited quite a while after I turned on HA again but all entities remain unavailable, battery powered and mains powered. If I restart HA then all entities become available again, almost immediately.
It does sound like a similar problem to mine. I think you should post a bug report in Home assistant as well, I think that may spike the developer in question to realize there’s something not quite right in the iniatialization process.
Come to think of it, I may have faced similar problems as you have. Only the first time after some tinkering I did not know what fixed it and the second time waiting fixed it, so I blamed my impatience. But the tinkering the first time was way too long to be the same, on second thought.
As you mentioned Phoscon, I assumed you used the official Deconz addon like me. You can report issues for that trough github here: Sign in to GitHub · GitHub