It seems rasa supports multiple domain files inside a folder called domain but won’t accept multiple files in the root folder. Meanwhile rasax supports multiple domain files if they are in the root folder but won’t accept them in a sub folder. Is there a way round this?
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Could you provide more information about your problem? 
What is your rasa and rasa x version and how do you deploy the rasa x instance (local mode/docker-compose/helm chart)?
If you initialize rasa x in local mode with the command rasa x --domain <the directory with multiple domain file>, rasa x should load domain files from the directory properly.
I am using the docker-compose rasa-x on a server. 0.42.6 version so I guess I can add that to the docker-compose file command and it will pick up the domain file. Thanks for pointing that out.