Installing MySQL from a noinstall Zip Archive - Should I Overwrite System Tables and Data?
After talking to some MySQL admins, I came to a conclusion on how to go about this. We can do the below steps:


Take a MySQL dump of all the databases
Overwrite all the installation folders, including the database folders and files
Re-apply the MySQL dump backup
Run mysql_upgrade


However, you may notice that there's no conceptual difference between the steps above, and simply not copying over the data file as part of the installation.

If you avoid copying over the data file, the steps become the following:


Overwrite all the installation folders, excluding the data folder.
Run mysql_upgrade