What is the correct way to upgrade packages?

I tried to upgrade Root package from Master Model version 6973 to 2021.1.1901. I replace (delete old and copy new files) the content of Root folder in current model and run Architect 2021.1.1901. But there is an error thrown after choosing configuration and indexing:

An error has occurred when trying to upgrade file: 
Class version written in persisted object is greater than current version of the class. 
This should never happen, please check version of Workflow in C:\OrigamModel\TEST2\Root\Workflow\ModelEntityColumnLookup_Label.origam

What is the correct way to upgrade system packages?
Thank you.

The version of the ModelEntityColumnLookup_Label.origam is newer than what Architect 2021.1 can read. You probably took the model from a newer master branch.

The file should look like this:

The best way is to check it out from the correct branch on GitHub