If a chatbot is using standard bot user and configured to use flow invocable actions in the Welcome or Main Menu dialogs, then the bot may transfer the session directly to an agent without executing those flows. This happens since standard bot user does not have access to run flows.
This may also be caused due to invalid input/output parameters on the invocable actions added to the Welcome or Main Menu dialogs or reference to elements such as a messaging component that may become invalid after bot migration from one org to another.
Add "Run Flows" permission to the chatbot permission set or assign a custom bot user with this permission enabled.
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