MySQL Group Replication - Offline Node with cluster Metadata 1.0.1
First of all, you are mixing some concepts. You are using MySQL InnoDB cluster which uses MySQL Group Replication as the replication technology.
I see that you have upgraded MySQL Shell version's and most probably you also upgraded the version of the MySQL servers of your cluster. The error you see when running cluster.rejoinInstance() is not related to Metadata but rather related to the incompatibilities of different MySQL versions in the Cluster. More info here: https://dev.mysql.com/doc/refman/8.0/en/group-replication-online-upgrade-combining-versions.html
How did you upgrade your instances? There's a procedure to follow. I'd recommend you to read the documentation regarding rolling upgrades: https://dev.mysql.com/doc/refman/8.0/en/mysql-innodb-cluster-upgrade.html
Regarding your scenario, my advice is to:

Use an older Shell version to remove the instance you're trying to remove, using cluster.removeInstance(). The version must be 8.0.18 or lower.

Using the latest MySQL Shell (8.0.21), upgrade the Metadata schema using dba.upgradeMetadata().


You will then have an operational cluster with the latest metadata schema version and you can then proceed to do the rolling upgrade of your instances and add them to the cluster as intended.
Cheers,
Miguel