So, you may have ''inherited'' some leftover identifier from the PROD server's repository when you copied it. This installer might be a bit picky about that.
We can fix your repository to leave that ''identifier'' behind.
Locate or create a link for Configuration Wizard (http://eyeontesting.com/questions/7793/where-is-the-link-for-configuration-wizard-on-alm1.html).
Then, MOVE your ''...repository'' folder to a totally different location and rename it, to something like ''d:1220repository''. If this is on the same drive letter, it should do this fairly quickly.
Then, re-run the Configuration wizard keeping current configuration, but specify for it to ''Connect to existing schema/ second node'' and confirm it is pointing to your 12.20 qcsiteadmin_db schema/db name (not a copy).
The mismatch error should go away and when complete, the installer will redeploy QC, start the QC service, and launch IE and Site Admin. But, now you will have a BLANK repository. Don't worry, you just have to put back the domain-level and project folders.
Stop the QC service and then MOVE your various domain folders (1220repositoryqcDefault'' and sibling folders) into the newly (installer) created repositoryqc folder. You can either replace the ''Default'' folder or move it's children folders (project folders) into the new Default folder. Also move the other domain folders (keeping their names the same) out from under ''1220repositoryqc'' and into the newly (installer) created repositoryqc folder.
To avoid confusion, delete the ''1220repositoryqc'' folder when you are done moving the DOMAIN-level and Project -level folders out of it.
Start the service and you should be upgraded to 12.21 and your repository back where it was originally where the projects can find them.
Reminder, 12.0 --> 12.21 upgrade does NOT require any project-level upgrading.