Hi Guiseppe,
You are right, Arcadia allows you to start at the logical level (even at the physical level if you want).
Also a good resource for starting:
https://esd.sutd.edu.sg/40014-capella-tutorial/index.html
Now I don’t see any reason why you should not be able to create and modify Functional chains through FCD diagrams.
What Capella version do you use? What Java version? What OS?
Would you be able to share your model, or a simplified version of it so that I can reproduce your problem and see what is happening?
Stephane