If you want to trigger Deep Clone with Jira Automation, we recommend to work with Deep Clone post functions and global looping transitions - meaning that the status of origin is also the status of destination.
This is how you can set up a Jira Automation with global looping transitions.
Add a global looping transition to your workflow.
Add a Deep Clone post function to the looping transition.
Create a new Jira Automation rule with an action that triggers the looping transition.
Define a transition match with the name of your global looping transition (e.g. Clone), to make sure that the correct transition is triggered.
Now you can trigger a Deep Clone via Jira Automation without changing the status of an issue.
Make sure that your automation rule doesn’t cause a loop that creates infinite clones. Issues that are created with Deep Clone can trigger automations of “Issue updated” rules.
Global looping transitions can be removed from the issue view by adding the condition “Hide from User” to the transition.
If Deep Clone and Automation overwrite each other, you could insert a ‘refetch issue data’ action immediately after the trigger in Automation for Jira. In ‘more options’ you can manually configure a delay which would solve your problem.