This might not be the best way but it works for me.
I found that if I go to File > Export Settings and then Save the settings in the config file. I can then open the file in a text editor and remove/edit the Favorites that I wanted to remove. Scroll down to where you see "<Favorites>" you can then locate the favorite that you want to delete. You will see the "<DisplayName>(Enter Name here)</DisplayName>" of the one to be deleted. Locate the "<Favorite>" immediately above it and delete everything through the "</Favorite>" immediately below it.
Then save the config file as a filename.config . Go back to the Cloudberry Explorer and go to File > Import Settings. For the "Accounts" and "Favorites" options change "Merge" to "Replace".