Get the UUID of the default profile
Substitute that value in to the second command to enable transparency level
$ dconf read /org/gnome/Ptyxis/default-profile-uuid
'3aae5a177777aa966b1fd63467153e2d'
$ dconf write /org/gnome/Ptyxis/Profiles/3aae5a177777aa966b1fd63467153e2d/opacity 0.85
Did your transparency stop working too? I used this method and it was working great, even now it still shows the transparency setting. However, now it just isn't transparent at all despite the setting.