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Whenever root stack gets stuck, it's advised not to touch any nested stack as that would even worsen the situation.
The only option that you can do is import resources into your stack by following the AWS Documentation but I doubt that would be feasible option for you.
Based on my extensive experience working with nested stacks, it's best to reach out to AWS Support and explain them the situation. They are well equipped to resolve the nested stack stuck issues from their end.
In your case, since you deleted nested stack, now it's less likely that AWS would be able to support you here. I'd take the backup of underlying resources such as database, s3 etc, delete the root stack and redeploy as fresh. This would be the best option to recover from this situation. I assume this is not the production environment.
Additional References:
Troubleshooting CloudFormation - AWS Documentation
Troubleshoot CloudFormation stacks that are stuck in progress
Fix CloudFormation stacks stuck in the cleanup state
Hope you find this information helpful.
Comment here if you have additional questions, happy to help.
Abhishek
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Thank you for you detailed answer. I have a question though: When deleting a resource through Amplify cli, the same thing happens, no? the nested stack gets deleted. If there's only a way for me to force create this nested stack through amplify cli it would solve the issue no ?. Because the nested stack is in DELETE_COMPLETE status and amplify is trying to UPDATE it (and it's throwing an error)
Your understanding is absolutely right. I was thinking, if you can afford to create the stacks all over again starting from Root stack, like delete the root stack and then redploy. Certainly not an elegant way of doing it, but just thinking to get out of this situation. If you have support plan to log a case, AWS support could certainly help you getting out of this situation, if you'd not have deleted nested stack, where they do update some internal linkage and ask you to run the updates and then link it again. Just a food for thought for future, consider adding Termination Protection for Cloudformation nested stack