To resolve the "Table doesn't exist" error during the MySQL upgrade I think you should follow below steps:
Run a Repair on Corrupted Tables: Use the mysqlcheck command to repair any corrupted tables before upgrading. Run the following command because this will check and repair any issues with the tables across all databases.
mysqlcheck -u root -p --all-databases --repair
Check for Missing Tables: Ensure that the table causing the error isn't missing or dropped. If it's important and missing, try restoring it from a backup, and if the tables are still corrupted and cannot be repaired using the above steps, in that case you can try Stellar Repair for MySQL because it’s a reliable tool that can fix corrupt .frm and .ibd files, and recover all your data without any loss.
Tip: Once the issue is resolved and the tables are repaired, rerun the pre-checks and proceed with the upgrade.