(From AWS Support)
Thanks for your patience during our investigation. I also tried to reproduce this in my environment as well and I am facing the same issue as well. Even with "show tables" I am able to see that tables exist in the database but still it gives error "ERROR 1146 (42S02): Table 'schemaname.tablename' doesn't exist". Here are my test results:

        - Took backup from MySQL Database using below command.
        sudo innobackupex --user=root --password=root1234 --stream=tar /tmp | gzip -9 >./mybackup.tar.gz

        - Copied mybackup.tar.gz file to Amazon S3 Bucket.

        - Initiated "Restore from S3" from the backup taken from my external MySQL Database.

        - Restore completed successfully and I was able to see tables in "show tables".

        - But still was facing  "ERROR 1146 (42S02): Table 'schemaname.tablename' doesn't exist" for all tables in Aurora database

After doing some more investigation, I was able to see that this is identified as an internal bug. Due to which data is stored in the metadata, but is missing from INFORMATION_SCHEMA INNODB_SYS_TABLES Table. I understand it was working fine earlier (till last Tuesday, 11-22), but it appears that it is because of new released patch on Aurora cluster. Since you mentioned that you restored all these three clusters recently (x,y, and z), which means they must be running on the most updated patch of Aurora which have issues in reading table that were restored using "Restore from S3" feature.

Our engineering team have already identified this bug and will be released on 12/08. Therefore I would request either to wait for this to be fixed during next release or you can use one of the workaround to import data to Aurora RDS instance as suggested in our public documentation [1].