Since nobody replied and I couldn’t find an answer, I decided to go back to a single domain file meanwhile.
But left the domain folder in the root of the project just in case, which means the folder was also uploaded on the GitHub repo which the server’s Rasa X pulls from.
So, on the server, I went to Rasa X’s “Domain” tab, only to find out that it automatically detected all the domain files in the folder as well as the original one.
So that’s solved 
As for the other part of the question, I posted it in a separate topic.