I just struggled with something like this myself. What I have found is that the act of “Saving” the Homekit Add-on inside the OpenHab3 UI causes some of the data to be lost when the config file is over written. Specifically the entires pertaining to MAC address and User Identifications. I would set up the binding with the suggestions above (Remove, clearPairings, Re-Add Bridge to HomeKit etc…) and still find my devices non-responsive after a while. Finally I figured out that the data was being lost when I was saving to make changes like such as to enable the use of mDNS. So I examined the config file and confirmed the discovery, I then after going through the process again to get it all set up correct then simply duplicated the config file just incase I clicked the save button again and lost all the specific data for users, If I did I can now replace with a good copy again and not lose the connection to my devices. I have at this point started to only modify the config file manually - it does require OpenHab3 rebooted to see the effects take place but I don’t lose my devices. I have now been running stable for approximately 5 days and everything is stable and works. I no longer get told by Siri that she can’t communicate with my OpenHab3 Devices.
Update
The Specific file to backup is located here, to recover if you lose the connection.