I have a question about the upgrade process. I hope you don't think it's a silly question, but I would just like a definite answer from someone who is qualified to answer.

Whether the upgrade is from 1.3.8a to 1.3.9g or 1.3.9? to 1.3.9g

If all of the upgrade files are uploaded, overwriting the old files, but the template over ride files have not been compared, merged and upgraded too, is the cart still considered to be upgraded?

I would think it's not a complete upgrade.