If you Deleted Schedule E from your Federal return, click on State in the left-side menu. This should make your Federal changes flow into your state return.
To make sure, click on Tax Tools > Tools, then 'Delete a Form' from the pop-up menu.
Scroll all the way down to your State Return to see the forms listed. You can delete here also.
More info:
https://ttlc.intuit.com/replies/3288508
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