Just increase Scale 1D your green object Inside because from the image we can see if it completly touching the surface! :)
Make Trim Keep the Surface and green Object
Join the 2 Object
You can make the regular Fillet or even a variable Fillet if you want

Better to post your 3dm file for be sure because an image is not sufficient! ;)
And we must remodeling all for verify so a big lost of time! (us and you for waiting the answer! ;)

Here with a big regular Fillet! :)