JM.
Thank you for the suggestion.
Unfortunately, I have not been able to validate a backup yet as I had planned to do a backup last night and B2 was down for maintenance. 
I tried to run one via CLI and that failed as discussed on this post, and so in summary, I have been unable to test whether backups work with Duplicati.
I am hoping to schedule and run a backup via the GUI this weekend.
I will look into the certificate situation in more detail although if the backup works then I might just ignore the errors.