You should not be worried. It was very simple for me.
Here is what I did.
MAKE BACKUP.
Disable products.
Upload file.
Run Script.
Revert templates and fix them.
Reenable products one by one.
That was what I did. When going from 3.6.1 to 3.6.2 I didn't even disable my hacks, and everything worked fine right from the get-go. No need to worry as upgrading has been made really easy.
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