It is advisable you avoid deleting those. But since you have already done it. This may help you rectify it.
First click on a domain in "Hosted Zones," What do you see? Well 4 name servers assigned to the hosted zone by Route 53.
This is what happens, every time you create a hosted zone, these 4 values will almost always be different. So new zones would mean new values. This is what is wrong in your case. Your system is still expecting the older values that were recorded. An updation is needed here.
Go to Route 53 and click "Registered Domains."
Select the concerned domain.
Select "add/edit name servers."
Enter new values this time.