Hi,
I believe this is still an ongoing issue. I have posted about this previously (Calibration for Wattbike Atom) …
The ‘not ideal but best workaround’ solution that I have found is to quickly open the pairing devices screen (by hitting the menu button and clicking on the paired devices), and deselecting/reselecting your Atom within the ‘Controllable’ box… Press the Menu button to return to the game and you will then be able to use the gears as normal.
It seems ERG mode stops the ‘gears’ on the Wattbike Atom working and any the signal to reactive the gears is not sent during a freeride section (where you require the gears). Hopefully they will resolve this soon.
Hope this helps.