We are working on separate modules where we want to deploy the RASA chatbot on multiple modules.
In order to do that, can we have multiple nlu.md files?
If not, how can we handle different Modules and specific Entities and Intents defined.
Yes, you can. You should use something like this (folder structure):
But be aware that Rasa X may have problems working with multiple NLU files at the moment (at least in my experience)
IIRC, Rasa X does support multiple NLU files. See here - How to run rasa-x on the mac?