I have (had) exactly the same problem.
I moved from a system booting on an SD card to a new system that boots from an SSD. For that matter I am using an Argon One M2. The SSD is connected to the lower USB3 port with the special plug provided.
After restoring my system, I plugged the ConBee II. It was recognized but communication with the ZigBee devices was not working anymore (even though all devices were still visible). I though it was a problem of backup so I decided to remove all the devices from the network and paired them again. Unfortunately, after testing several devices none were able to be paired.
I did some search on the net and apparently the ConBee plug does not like to be used on a RPi that boots on an SSD.
Then I found your message and I have looked at the video that you mentioned and applied the recommendation of using an USB extension cable and now it works!
In fact, I was already using an extension cable and the ConBee stick was at about 30-40 cm from the RPi and now it is at about one meter. I am skeptical about the need to have a “minimum distance” between the SDD and the stick? I would be surprised that an SDD produce enough “radiation” to prevents the ConBee to work.
Maybe (probably) what makes the difference is that at the same time I moved the ConBee from the second USB3 port to one of the free USB2 port.
I am using ZHA to drive the ConBee and I looked at the log file from HA core. I had the following messages repeating:
2021-12-10 17:23:42 ERROR (MainThread) [zigpy_deconz.uart] Lost serial connection: device reports readiness to read but returned no data (device disconnected or multiple access on port?)
2021-12-10 17:23:42 WARNING (MainThread) [zigpy_deconz.api] Serial '/dev/serial/by-id/usb-dresden_elektronik_ingenieurtechnik_GmbH_ConBee_II_DE2234672-if00' connection lost unexpectedly: device reports readiness to read but returned no data (device disconnected or multiple access on port?)
This clearly indicates that the device is seen but communication with it is not possible. Now the message is gone. I have already paired some router and end devices without problem.
This is a very strange problem but I would like to be sure what is causing it. So, I will probably make the following tests to be sure what is really causing the problem:
The bad news is that now I have to rebuild my network … But at least it works
As you already tried to move away the stick, try to put it on one of the USB2 port and let me know if it works