Hi Neil,
Funnily enough (not funny really, sorry), I experienced the same thing recently when I reconnected my long running ATOM after having temporarily removed the Pi/Bridge unit to use the antennas and dongles to set up another station.
Replaced my original unit after I had finished, booted it up and re-ran the config with the dongles in Upper and Lower Left (which is where they always were) and got the same 'device 0 with serial number 1090 cannot be found' message.
Checked the dongles were in the correct slots and properly located then rebooted - this time all fine but still had to reconfirm 'use dongle 0 as 1090'. Rest of config went as expected and (AFAIK) the station has been running fine since (now well over a week). Oh and mine is still on a daily timer - off overnight.
Not sure how much this helps, but obviously something we need to keep an eye on.
Regards
Peter