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You can delete the plan without worry, the Jira issue data is not going to be altered by the removal of the plan.
Portfolio pulls the data sources from the jira issue and commits the data back to Jira on approval so when a plan is deleted only the portfolio specific data, or data that has not been committed is affected from the issue, exe the team field will be removed, or any changes to the data on the plan that has not yet been committed/saved.
When recreating a plan it will repopulate the data as you modify the plan and commit new values.